Re: [gmx-users] Calculating diffusion coefficient in three dimension
search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] strange lincs warning with version 4.6
the neighbor list ns_type = grid; Make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor rlist = 1.4; cut-off distance for the short-range neighbor list coulombtype = PME; Fast Particle-Mesh Ewald electrostatics rcoulomb= 1.4; cut-off distance for the coulomb field vdwtype = cut-off rvdw= 1.4; cut-off distance for the vdw field fourierspacing = 0.12; The maximum grid spacing for the FFT grid pme_order = 6; Interpolation order for PME optimize_fft= yes pbc= xyz Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 300 energygrps = Protein Non-Protein Pcoupl = no;berendsen tau_p = 0.1 compressibility = 4.5e-5 ref_p = 1.0 nstpcouple= 5 refcoord_scaling= all Pcoupltype = isotropic gen_vel = no;yes gen_temp= 300 gen_seed= -1 Thanks a lot Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] which version it is
Hi, As I understand it, the current and most up to date CHARMM protein force field (as included in both the charmm27 and charmm36 force field directories) is the CHARMM22 protein force field with the CMAP correction. In other words there would be no difference between the two options originally mentioned. Cheers Tom ABEL Stephane 175950 wrote: Hi, Probably the CHARMM27_protein+Charmm36_lipids version. AFAIK, the second version was not already converted in GROMACS format. Stephane --- hello: I found a charmm36.tar.gz in Gromacs website GROMACS 4.5.4 version of the CHARMM36 force field files. These updated CHARMM lipids allow the all-atom simulations of membrane and membrane-protein systems without the use of surface tension. Check out the forcefield.doc for more information regarding these files 71.65 kB15:42, 25 Sep 2012TomPiggot I am just wondering, is the the one with CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids? thank you very much best Albert -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] which version it is
I must have missed that one, thanks for the link! So, to confirm, the protein force field in the CHARMM36 force field contribution is the CHARMM22 protein force field with the CMAP correction. The contribution is just for the updated CHARMM36 lipids. Cheers Tom Justin Lemkul wrote: On 11/19/12 11:28 AM, Thomas Piggot wrote: Hi, As I understand it, the current and most up to date CHARMM protein force field (as included in both the charmm27 and charmm36 force field directories) is the CHARMM22 protein force field with the CMAP correction. In other words there would be no difference between the two options originally mentioned. There is indeed a CHARMM36 protein force field that is distinct from the one included in CHARMM27 (which is, as you say, CHARMM22 + CMAP). http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflatNumber=30472 -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] which version it is
Hi Stephane, The confusion was my fault, I did not realise that there were newly developed CHARMM36 protein parameters (Justin kindly pointed this out). You were quite correct that the contribution only contains the update for the lipids. Cheers Tom On 19/11/12 18:49, ABEL Stephane 175950 wrote: Hi Thomas and Justin, I agree with you, but I think that Albert asked if the GROMACS 4.5.4 version of the CHARMM36 force field files contain the newly developed parameters for protein (also called CHARMM36) and described in Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., MacKerell, A. D. (2012). Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2 dihedral angles. Journal of Chemical Theory and Computation, 120718184839007. doi:10.1021/ct300400x I said no Sorry if it was not clear in my previous message Stephane -- Message: 1 Date: Mon, 19 Nov 2012 16:14:48 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] which version it is To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af02d1c...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii Hi, Probably the CHARMM27_protein+Charmm36_lipids version. AFAIK, the second version was not already converted in GROMACS format. Stephane --- hello: I found a charmm36.tar.gz in Gromacs website GROMACS 4.5.4 version of the CHARMM36 force field files. These updated CHARMM lipids allow the all-atom simulations of membrane and membrane-protein systems without the use of surface tension. Check out the forcefield.doc for more information regarding these files 71.65 kB15:42, 25 Sep 2012TomPiggot I am just wondering, is the the one with CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids? thank you very much best Albert -- Message: 3 Date: Mon, 19 Nov 2012 16:28:28 + From: Thomas Piggot t.pig...@soton.ac.uk Subject: Re: [gmx-users] which version it is To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50aa5e2c.4000...@soton.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, As I understand it, the current and most up to date CHARMM protein force field (as included in both the charmm27 and charmm36 force field directories) is the CHARMM22 protein force field with the CMAP correction. In other words there would be no difference between the two options originally mentioned. Cheers Tom ABEL Stephane 175950 wrote: Hi, Probably the CHARMM27_protein+Charmm36_lipids version. AFAIK, the second version was not already converted in GROMACS format. Stephane --- hello: I found a charmm36.tar.gz in Gromacs website GROMACS 4.5.4 version of the CHARMM36 force field files. These updated CHARMM lipids allow the all-atom simulations of membrane and membrane-protein systems without the use of surface tension. Check out the forcefield.doc for more information regarding these files 71.65 kB15:42, 25 Sep 2012TomPiggot I am just wondering, is the the one with CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids? thank you very much best Albert -- Dr Thomas Piggot University of Southampton, UK. -- Message: 4 Date: Mon, 19 Nov 2012 11:34:28 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] which version it is To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50aa5f94.6090...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/19/12 11:28 AM, Thomas Piggot wrote: Hi, As I understand it, the current and most up to date CHARMM protein force field (as included in both the charmm27 and charmm36 force field directories) is the CHARMM22 protein force field with the CMAP correction. In other words there would be no difference between the two options originally mentioned. There is indeed a CHARMM36 protein force field that is distinct from the one included in CHARMM27 (which is, as you say, CHARMM22 + CMAP). http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflatNumber=30472 -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 5 Date: Mon, 19 Nov 2012 16:48:27 + From: Thomas Piggot t.pig...@soton.ac.uk Subject: Re: [gmx-users] which version it is To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50aa62db.8010...@soton.ac.uk Content-Type: text/plain
Re: [gmx-users] Problem with equilibrated lipid bilayer structure
Hi Jernej, You can have a look at our paper linked by both Peter and Sebastien earlier in this thread, which has a detailed methods section. Alternatively search in the GROMACS mailing list archives, as this has been discussed in detail before. Cheers Tom Jernej Zidar wrote: Hi Tom, Thanks for the detailed reply. Could you please suggest the appropriate cut-offs and/or parameters I should use? Thanks, Jernej On Mon, Oct 15, 2012 at 5:46 PM, gmx-users-requ...@gromacs.org wrote: Subject: Re: [gmx-users] Problem with equilibrated lipid bilayer structure To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 507bda00.8060...@soton.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Jernej, The CHARMM force field was developed for use with the TIP3P model making this probably the appropriate choice, even if this model may not perform the best for simulations of pure water (see http://pubs.acs.org/doi/abs/10.1021/jz200167q for some more details). As for some specific GROMACS points with the CHARMM36 lipids. Firstly I recommend you to use the CHARMM TIP3P variant and secondly you should also be careful with the cut-off's you choose. I do not think a dispersion correction would be appropriate and you should also probably be using some different cut-off's to those you give in you mdp (typically a switching off of the van der Waals interactions is done with this force field). Finally you also need to be careful constraining all bonds (instead of just bonds to hydrogen atoms) with this force field. We found that we needed to increase the accuracy of the LINCS settings when constraining all bonds to ensure energy conservation. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
Hi James, The bilayers from the CHARMM-GUI can be converted into any force field using a simple script. For a united-atom force field you will need to remove the non-polar hydrogens, rename the atoms and possibly reorder some of the atoms in the lipids. As for other methods to build membranes, there are numerous different methods available. One of the simplest approaches is to use genconf to replicate a single lipid up to the desired size of membrane and perform and simulation to equilibrate the properties of your membrane (although depending upon the lipid and force field this may require simulations in the order of several hundreds of ns though). Another fairly simple method (which can also be easily used to make hexagonal membranes) is to self-assemble a coarse-grained membrane, map that back to an atomistic representation (using one of a number of available tools) and equilibrate. One issue using this method is that the self-assembly often results in uneven numbers of lipids per membrane leaflet. This, however, is easy to correct after the self-assembly. Cheers Tom James Starlight wrote: Dear Felipe, thanks for advise. Does the Packmol software suitable for generation coordinates of the bergers ( for gromos 56 ff) lipids ? As I know CHARMM-GUI membrane builder is suitable for only CHARMM force field lipids. James 2012/10/4 Felipe Pineda, PhD luis.pinedadecas...@lnu.se: To generate starting (non-equilibrated) bilayer structures for use in MD simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. Otherwise, for conventional lipids CHARMM-GUI membrane builder (http://www.charmm-gui.org/?doc=input/membrane). Hope it helps! Felipe On 10/04/2012 07:46 AM, James Starlight wrote: Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reference for CHARMM36 Force Field Conversion
Hi everyone, This message is just to let people know that there is finally a reference that we ask you to cite if you publish work using the CHARMM36 lipid force field contribution available from the GROMACS website. The reference is provided in a new version of the forcefield.doc file, and is also given below: Thomas J. Piggot, Ángel Piñeiro and Syma Khalid Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study Journal of Chemical Theory and Computation DOI: 10.1021/ct3003157 http://pubs.acs.org/doi/abs/10.1021/ct3003157 A validation of the conversion for DPPC and POPC membrane systems (in terms of single point energies calculated in both GROMACS and NAMD) is provided in the supporting information of this work. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer
Hi, The experimental range of diffusion coefficients are quite large for DPPC, plus the force field and simulation parameters can have a large impact upon the diffusion speeds seen in the simulations. We have just published a study comparing force fields for simulating DPPC and POPC membranes and further details on differences in lipid diffusion are provided in the paper: http://pubs.acs.org/doi/abs/10.1021/ct3003157 We did not test this exact set of cut-offs with this force field. However, from the tests we did perform using these Berger DPPC parameters, I expect that the diffusion speeds should fall within the experimental range using this set of cut-offs. As for the area per lipid, what you are seeing is pretty much as I would expect with the 1.2 nm cut-offs and a dispersion correction. If you want a higher area per lipid, you could try removing the dispersion correction or reducing the cut-off (with the dispersion correction, we saw sensible membrane behaviour with 1.0 nm cut-offs). Do be sure to check the lipid diffusion rate is still sensible if you remove the dispersion correction, as it should substantially increase when doing this (see the paper for some more details). Cheers Tom On 12/09/12 16:29, Justin Lemkul wrote: On 9/12/12 10:56 AM, David Ackerman wrote: Hello, I have been basing some DPPC bilayer simulations off of files from Justin Lemkul's tutorial, including the .itp files and .mdp files. Everything has been working fine except that my area/lipid seems to be too low and my diffusion coefficient seems to be too slow compared to experimental values. As a test, I just started with Tieleman's How far off are the diffusion constants? I have never had a lot of luck reproducing experimental values, but this may reflect a limitation of the parameter set, simulation length, or both. equilibrated 128 DPPC bilayer system, including the waters, and ran a simulation using the mdp file below (note though I selected continuation=yes, this was in fact not continued from a previous equilibration). The simulation has been running for ~75 ns so far, and the area/lipid is on average ~.61-.62 nm^2 . When I do full That sounds like the expected outcome for this force field. Why do you say that is too low? temperature/pressure equilibrations, even using different thermostats/barostats, I seem to get area/lipid values similar to these. Also, my diffusion coefficients are smaller than those reported in papers invovling DPPC bilayers. I was wondering what the possible reasons for this could be. Any help you could provide would be great. Curiosities in the .mdp file: tcoupl = Nose-Hoover ; Less accurate thermostat tc-grps = DPPC SOL ; three coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each Why is your tau_t so small? Generally one should use 0.5 - 2.0 with Nose-Hoover. group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 1.0 ; time constant, in ps ref_p = 0.0 1.0 ; reference pressure, x-y, z (in bar) Why are you setting zero pressure along the x-y plane? compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off If you are not continuing from a previous run (as you say above) and you are also not generating velocities, you may be delaying equilibration by allowing the initial forces dictate the velocities. I suppose if the run is stable enough, this is not a huge problem, but in general this combination is not recommended. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer
by allowing the initial forces dictate the velocities. I suppose if the run is stable enough, this is not a huge problem, but in general this combination is not recommended. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer
Hi Chris, I'm not so sure as to say that all of the parameters for simulating lipid membranes were not developed with a dispersion correction. The Berger parameterisation used a dispersion correction for the pentadecane simulations which were used to parameterise the tails (although as far as I can tell from the Berger paper, this correction was not used in the DPPC membrane simulations). Furthermore, the GROMOS 53A6 parameters of Kukol were tested using simulations which applied a dispersion correction (although you could argue that these GROMOS parameters were initially developed without this correction) and if I remember correctly the CHARMM27 (but not CHARMM36) lipid parameters were intended to be used with a dispersion correction applied (although these parameters are not for use with NPT simulations). I would still argue that above all else, you should choose parameters that someone has shown to accurately reproduce the experimental membrane properties, irrespective of whether that is the original parameterisation work or not (it may well just be your own simulation tests). The Berger force field is a good example of where this sort of testing/validation has been important. Several papers have shown that PME should be used with this force field and not the direct 1.8 nm coulombic cut-off used by Berger et al. Furthermore, in our work I mentioned before, we show that with a 1.0 nm cut-off and no dispersion correction (so the van der Waals parameters I believe were used in the Berger DPPC simulations) there are several membrane properties that do not match the experimental range. I do agree with you for the example here though, it seems (from the information provided) the dispersion correction should not be included with 1.2 nm cut-offs (and this also agrees with results from three different cut-offs tested with the Berger force field in our work). Cheers Tom On 12/09/12 19:30, Christopher Neale wrote: While dispersion correction is a great idea that helps to reduce the impact of the precise choice of cutoff distance on the results, the Berger parameters (and indeed all other parameters) were not developed with the inclusion of dispersion correction and one could argue that it is thus non-optimal to include dispersion correction here... especially since it leads to poorer results. This is separate from the difference between isotropic dispersion correction and a proper PME-type LJ term. Both of which are expected to lead to smaller APLs. When using anisotropic pressure coupling for lipid bilayers, you should use 1 atm in all dimensions. Chris. -- original message -- Right I guess my biggest concern was diffusion. I did in fact do 12 simulations of DPPC bilayers for 100 ns each, and still got the aforementioned APL and diffusion. When I turn off the dispersion, I get more appropriate APL and MSD values, that match other papers, even when only looking at one simulation. To me, it does not seem the mdp file I used is able to get more common APL and diffusion values even when averaging over a large number of simulations. As for the pressure in the x/y direction, is it more appropriate to use 1 atm or 0 atm for bilayer simulations? -David -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ParmBSC0 Force Field Contribution
Hi everyone, Just so people know, I have added to the user contributions section of the website to include the AMBER ParmBSC0 nucleic acid parameters in GROMACS 4.5.x format (see http://mmb.pcb.ub.es/PARMBSC0/ for further details regarding these nucleic acid parameters). The modified dihedral parameter conversion was validated through a comparison of single point energies in GROMACS and AMBER (see the paper below for further details). If you use these files we also ask that, in addition to the original force field publications, you also cite: Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study Andrew T. Guy, Thomas J. Piggot, and Syma Khalid Biophysical Journal Volume 103, Issue 5, 5 September 2012, Pages 1028–1036 http://dx.doi.org/10.1016/j.bpj.2012.08.012 Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] When to use Dispersion Correction for Lipid Bilayers
Hi, In addition to the Michael's comments, I saw an interesting poster about this sort of inclusion for the long-range van der Waals interactions at the Biophysical Society annual meeting earlier this year. A link to the abstract for the poster is below. I guess this should become available in GROMACS at some point soon. http://www.cell.com/biophysj/fulltext/S0006-3495%2811%2902284-3 Cheers Tom Michael Shirts wrote: Short answer -- use a dispersion correction if the force field was parameterized to include one. Make sure you use the cutoff that the lipid was parameterized for as well. Long answer -- neither on nor off is correct for a lipid bilayer. A dispersion corrections corrects for the fact that you are neglecting the r^-6 term at long range. However, it assumes an isotropic distribution outside the cutoff. Lipid bilayers have long range order, so a standard dispersion correction is inappropriate. The lipid properties will be cutoff dependent, which is not a very good thing. See PJ in't Veld, AE Ismail, GS Grest, J. Chem. Phys. 127, 144711 (2007) for a solution, using Ewald summation for the Lennard-Jones terms. This is in the works for Gromacs (and has been for a while), but might still be a while because it's a little lower on the to do list. Once methods like this are in, it will be possible to parameterize lipids that behave correctly. Best, Michael On Sun, Aug 19, 2012 at 3:16 PM, David Ackerman da...@cornell.edu wrote: Hello, I was wondering when it is appropriate to use Dispersion Correction for lipid bilayers, or which setting (no, EnerPres, or Ener) is best. I have seen it used in some discussions, and not used in others. As for myself, I have simulated a DPPC bilayer. With DispCorr=EnerPres, I get an area per lipid of ~.615 nm^2 (whereas other reported values are closer to .64 nm^2) and slower diffusion than is reported. However, when I don't have a DispCorr term, my area per lipid becomes ~.656 nm^2 and my diffusion more closely matches other reported values. So, should DispCorr be used at all for bilayer simulations, and if so, which type is most appropriate? Thank you for your help, David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
Hi, As I suggested earlier in this thread, I think the original poster should run test simulations of a CHARMM36 POPE membrane using either the NAMD or CHARMM softwares. It has been mentioned a couple of times in the thread thay there are differences in the implementations of the switching methods for the van der Waals interactions between softwares, and in my opinion this is one potential cause of the low area per lipid for the POPE membrane. This can be tested from these simulations in NAMD or CHARMM. Another potential explaination is that the relatively short simulation of Klauda et al. (40 ns) was not converged. As for other POPE force fields, the standard Berger parameters will not perform well. There are some force fields that have been reported to perform well. Apart from a couple of GROMOS ones I know of (GROMOS-CKP and GROMOS 43A1-S3 - I have used these in the past and both behave well at 313 K, which is well above the gel-liquid crystal phase transition temperature of 298 K), all-atom AMBER lipid parameters have been recently reported that include POPE (http://pubs.acs.org/doi/abs/10.1021/ct300342n). This may be another option that could be used for these simulations, with an AMBER force field used for the protein. Cheers Tom On 15/08/12 20:09, Peter C. Lai wrote: On 2012-08-15 06:55:59PM +, Christopher Neale wrote: Write the authors of the simulation paper that has a correct APL for POPE and ask them for an input file. That is really the only way to be sure that you are not doing something different than they did. In my experience, people are quite willing to provide you with their input file(s). If you still get a different APL than they reported, then see if your simulation times are similar and repeat your run a few times to see if it's just statistical noise. The fundamental problem Sebastian will have is that Klauda obtained their APLs using CHARMM software, and he is trying to reproduce this using the forcefield in Gromacs software. So even if the CHARMM input files were provided, it maybe difficult to exactly reproduce the conditions in Gromacs (if certain parameters were implemented differently) Regarding 323 K, I don't recall... it's just a number that sticks in my head. Perhaps it is for DPPE or DPPC. I'd still suggest that you at least try POPC. So your peptide binds more favourably to POPE than to POPC... that alone does not limit you to POPE. Then again, I don;t know exactly what you are trying to do. Chris. It is generally a good idea to use a higher temp than the phase transition temperature, since during equilibration close to the phase transition temp there is a risk of inducing some ordering due to uneven heating. People run DPPC at 323 because its phase transition temp is 315K. If POPC's is 271 and people typically run POPC at 300, then it may be wise to bump up the running temp of a POPE system. Of course, your APL will inflate at higher temperatures... -- original message -- My peptide is known to be more favorably to PE than PC membrane that is why I am using POPE. Experimentally, the liquid phase transition is at 298K for POPE (if I am not mistaken). Is your 323K refer to some simulations? At first I wanted to use the new CHARMM36 lipids parameters because they are supposed to solve the previous CHARMM27 issue with the area per lipid. However, I am consistently obtained smaller APL then experiment and I am not able to reproduce the published APL obtained for POPE, even if I am starting from their equilibrated 80-POPE membrane and use same simulation conditions. That was the reason for starting this thread on the mailing list. Unfortunately, my peptide conformational space in solution is only well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as they do not have APL inconsistency and are united-atom. I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be made neglegible by using bigger membrane compared to my peptide's size (?). Sebastien -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post
Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Gromacs 54a7 force field
Hi, Justin, I am interested by your comments regarding the CHARMM lipids. In particular can you elaborate as to why you think that the CHARMM lipids are better than the united-atom ones (such as Berger and several GROMOS variants). As for the original question, the modifications in going from GROMOS 53A6 to 54A7 will not influence the combination with the Berger lipid parameters, if the most common approach of using the parameters from the 'lipid.itp' file is taken. The interactions between protein and lipid will remain the same, with the van der Waals interactions between the protein and lipid treated using the GROMOS87 parameters as defined in lipid.itp. From my experiences I would strongly recommend using 54A7 over 53A6, as we have seen instability in short helices in 53A6 that is not reproduced when simulating the same systems with several other force fields. For the 'best' force field to choose when simulating a membrane-protein system, there is no definitive answer that I (or anyone else) can give you (yet). My own opinion is that currently CHARMM36 is probably too slow (given that I would strongly recommend the use of the CHARMM TIP3P water model with this force field) and that the all-atom protein force fields are probably better than the united-atom ones. This means that I would (for a PC membrane) use Berger for the lipids with OPLS-AA/L or an AMBER force field for the protein. This is just my (current) opinion though, I strongly suggest doing lots of your own reading before making your mind up. Cheers Tom On 18/07/12 22:55, Justin Lemkul wrote: On 7/18/12 5:51 PM, Rajat Desikan wrote: 54A7 also introduced changes to the Gromos96 lipid parameters How will this change my inclusion of the berger lipid parameters? Any thing that I should pay special attention to? Are there other lipid parameters more compatible? There are better force fields for lipids, but they require the use of CHARMM. There may be other suitable united atom force fields. My comment was intentionally generic; I don't know how well 54A7 pairs with the Berger parameters. In theory, it should be fine, but since Gromos96 parameters for lipids have been tweaked, maybe the balance of forces in the parameters for proteins and lipids will be affected. There was a new lipid atom type introduced to make Gromos96 lipids better. They're still not as good as CHARMM, though. I heard from a faculty member at our Institute that the 53a6 is a bad ff for a protein with a lot of alpha helices for longer simulations. She apparently saw the helices unravel when they were supposed to be stable. This is a hot topic. Conventional wisdom does demonstrate that 53A6 destabilizes helices, but others will contend that 53A6 is perfectly suitable for reproducing many experimental observables, including NMR signals. I tend to think that there is some bias, but all force fields have shortcomings. 54A7 is certainly better in terms of helical stabilization, from what I can see. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Gromacs 54a7 force field
Hi, Yes, I agree with you regarding the combination of Berger and GROMOS force field and requiring validation. I just wanted to point out the interactions between the protein and lipid are treated in the same way, irrespective of the different GROMOS protein force field used (when using the parameters from lipid.itp). Further on the topic of validation, the only work I know of that has studied in detail the Berger/GROMOS combination (doi:10.1088/0953-8984/18/28/S07) says that when using the standard method as employed by the parameters in lipid.itp: the strength of interactions between hydrocarbon lipid tails and proteins is significantly overestimated, causing a decrease in the area per lipid and an increase in lipid ordering So the standard approach is probably not the most appropriate way to combine the Berger lipids and the GROMOS protein force field. Rather using combination rules (as for example done in the Berger/OPLS combination) is probably better. Cheers Tom On 19/07/12 00:15, Justin Lemkul wrote: On 7/18/12 6:57 PM, Thomas Piggot wrote: Hi, Justin, I am interested by your comments regarding the CHARMM lipids. In particular can you elaborate as to why you think that the CHARMM lipids are better than the united-atom ones (such as Berger and several GROMOS variants). I think there's nothing wrong with Berger lipids, and I myself use them routinely. They do a decent job of reproducing lipid behavior, no question. My own use is motivated by historical reasons primarily since I began work with them many years ago (also around the time that 53A6 was all shiny and new) and I'm trying to keep consistent. It seems to me that the CHARMM36 parameters are very thoroughly validated and are very modern. The Berger lipids were developed a long time ago using very short (by modern comparisons) simulations and old parameter sets that have since been improved upon. There are numerous reasonable lipid models out there, to be sure. As for the original question, the modifications in going from GROMOS 53A6 to 54A7 will not influence the combination with the Berger lipid parameters, if the most common approach of using the parameters from the 'lipid.itp' file is taken. The interactions between protein and lipid will remain the same, with the van der Waals interactions between the protein and lipid treated using the GROMOS87 parameters as defined in lipid.itp. From my experiences I would strongly recommend using 54A7 over 53A6, as we have seen instability in short helices in 53A6 that is not reproduced when simulating the same systems with several other force fields. I agree with this, I'm just a stickler for validation. A test system using this force field combination should certainly replicate some known behavior. It's generally accepted that any Gromos derivative is compatible with the Berger parameters, but I've never seen anyone demonstrate it systematically aside from their own usage for particular cases. For the 'best' force field to choose when simulating a membrane-protein system, there is no definitive answer that I (or anyone else) can give you (yet). My own opinion is that currently CHARMM36 is probably too slow (given that I would strongly recommend the use of the CHARMM TIP3P water model with this force field) and that the all-atom protein force fields are probably better than the united-atom ones. This means that I would (for a PC membrane) use Berger for the lipids with OPLS-AA/L or an AMBER force field for the protein. This is just my (current) opinion though, I strongly suggest doing lots of your own reading before making your mind up. Indeed. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Berger lipid
Hi Shima, The lipids.rtp file in the charmm36.ff folder has many different entries for lipids. All you need to do is to run pdb2gmx with just one of your lipids of interest. This will produce a .top for this one lipid which is trivial to convert into an .itp (see Chapter 5 of the manual). Cheers Tom Peter Lai wrote: Uh didn't we go through all of this like more than a month ago? I published a paper using C36 POPC and even a linked to my popc.itp for it on this list... Of course Shima is welcome to pdb2gmx his own POPC, which I am fairly certain will result in an identical file... Lipidbook seems to only have C36 POPE. I guess maybe I will upload ours. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, June 28, 2012 7:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Berger lipid On 6/28/12 8:54 PM, Shima Arasteh wrote: Yes, I know that as studied the Kalp15 tutorial. Sorry, the last question :) : DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it ok? Because I see that POPC.itp is also required for simulation of protein in bilayer. You need a topology of some sort. It depends on what parameters you have on hand. If you do not have popc.itp from anywhere, then you need to generate it somehow. If it is present in the .rtp file for CHARMM36 that you have, then you can run pdb2gmx on it. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Trajectories
Hi, I think Erik meant to say that the program is trjorder (not g_order) for the ordering of molecules by distance. Cheers Tom On 05/06/12 14:41, Erik Marklund wrote: 5 jun 2012 kl. 15.05 skrev Justin A. Lemkul: On 6/5/12 9:02 AM, rankinb wrote: I am interested in pulling out the trajectories (x,y,z coordinates) of water molecules within a certain distance of my solute molecule. I have tried using g_select, but that will only give me the atom numbers and not the trajectories. I can create an index file using this command but unfortunately each time frame is set as a different group. Is there a way to get the trajectories at all frames of only the water molecules within a specified distance of a solute molecule? At present, there is no elegant way to construct such a trajectory, since, in principle, each frame can have a different number of atoms based on which water molecules satisfy the given criteria. Each index group that g_select provides corresponds to an individual frame in the original trajectory, which you can use to pull out individual coordinate files. Perhaps a multi-frame .pdb or .gro file would work, but I believe that .xtc and .trr files have to have the same number of atoms in each frame to be interpreted correctly. -Justin g_order orders the molecules according to distance to solute. Then you can pick out the N first from each frame. It is, however, a bit cumbersome for an entire trajectory. Erik -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se mailto:er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: dangling bond at at one of the terminal ends
Hi, You may also need to name your terminal DNA residues appropriately in your pdb file, as for the AMBER force fields the terminal DNA residues are named differently. Check out the dna.rtp file for these naming conventions. Cheers Tom On 03/06/12 14:50, Justin A. Lemkul wrote: On 6/3/12 9:47 AM, ramaraju801 wrote: HI, everyone am working on a system consisting of protein-DNA complex,where an protein comes and binds to the DNA to form a complex. To produce an topology file in gromacs i gave the command pdb2gmx -f XXX.pdb -o XXX.gro -p XXX.top -ter -ignh -ff amber99 . its creating the topology files of the protein but when its starts creating the topology file for the DNA seq its recognizing the starting and the ending terminus residue. and then stops giving an error Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried editing the .n.tdb and .c.tbd files by writing the terminal residues of DNA in those files but then its giving an error which says need an directive before the residue must been and old file Editing these files won't actually help, I don't think. The .n.tdb and .c.tdb contain terminal replacement instructions for proteins. For DNA, you should not need them. The error is more indicative of missing atoms. Consult the .rtp entry for your terminal nucleotides - you need to have all the atoms present and named as the force field expects them to be. You can't have anything missing or anything extra. Also, copying and pasting error messages directly from the terminal is vastly more helpful than a description. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Lipid A Topology
Hello everyone, As a follow up to my message last week regarding the addition of phospholipid (PC, PE, PG and Cardiolipin) topologies to the Lipidbook website, I am happy to announce that we have also added parameters for lipid A from E. coli. Lipid A is the lipidic component of lipopolysaccharide, which is found in the outer membranes of Gram-negative bacteria. If you use these parameters please read and cite the following work: Electroporation of the E. coli and S. aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes Thomas J. Piggot, Daniel A. Holdbrook, and Syma Khalid J. Phys. Chem. B 2011, 115 (45), pp 13381–13388 http://pubs.acs.org/doi/abs/10.1021/jp207013v To access the parameters you can use the following link: http://lipidbook.bioch.ox.ac.uk/package/show/id/62.html In addition, these parameters will soon be made available on our group website (http://www.personal.soton.ac.uk/sk2x07/index.php), along with a structure file for this molecule. Cheers Tom Piggot -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] forcefields for lipids
Hi Joakim, I am interested to know what other lipids this force field has been extended to include. Do you have parameters for unsaturated lipid tails and other classes of phospholipid (such as PE and PG)? Cheers Tom Joakim Jämbeck wrote: Hi, have a look at out recently developed all-atom force field. It is compatible with AMBER force fields for proteins (ff99SB, ff99SB-ILDN and ff03). The compatibility was tested via microsecond simulations of a peptide embedded in a bilayer. The paper describing the peptide simulations along with an extension of the parameter set has been submitted, but for now have a look at this published paper: J. Phys. Chem. B, 2012, 116 (10), 3164-3179, doi: 10.1021/jp212503e All our parameters are available at on Lipidbook. Let me know if you need anything else! Best, J -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] forcefields for lipids
Thanks Joakim, I will be very interested to see how these different lipids behave. This looks like it could be a really useful force field. We have also developed some parameters for PE, PG and Cardiolipin lipids which you might want to have a look at (for comparison with your ongoing parameter development). Details regarding the behaviour of these lipids are in the supporting info of this paper (http://pubs.acs.org/doi/abs/10.1021/jp207013v). Cheers Tom Joakim Jämbeck wrote: Hi Tom, we have parameters for unsaturated tails now as well as for PE lipids ready for use, the manuscript for these have been submitted. PG and PS lipids are on the way and parameters for cholesterol and sphingomyelin are finished now and the manuscript should be finished relatively soon. Best, J On May 22, 2012, at 15:40 , gmx-users-requ...@gromacs.org wrote: Date: Tue, 22 May 2012 13:49:48 +0100 From: Thomas Piggot t.pig...@soton.ac.uk Subject: Re: [gmx-users] forcefields for lipids To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fbb8b6c.70...@soton.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Joakim, I am interested to know what other lipids this force field has been extended to include. Do you have parameters for unsaturated lipid tails and other classes of phospholipid (such as PE and PG)? Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] forcefields for lipids
Hi Shima, Yes, the phospholipid parameters are available to use. I am currently in the process of uploading them to the Lipidbook website. If you check this website soon they should be available to download (DPPE and POPE parameters and bilayers are already there). For accessing them on Lipidbook the name of the force field is the GROMOS-CKP lipid force field. The parameters are consistent for use with the GROMOS 53A6 and GROMOS 54A7 protein force fields for simulating membrane proteins systems. I should also note that the Kukol DMPC and DPPC parameters (http://pubs.acs.org/doi/abs/10.1021/ct8003468) are also consistent with these phospholipid parameters, if you wish to simulate mixed lipid bilayers. Cheers Tom Shima Arasteh wrote: Is this FF available for others to use? Thanks. Sincerely, Shima *From:* Thomas Piggot t.pig...@soton.ac.uk *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, May 22, 2012 7:39 PM *Subject:* Re: [gmx-users] forcefields for lipids Thanks Joakim, I will be very interested to see how these different lipids behave. This looks like it could be a really useful force field. We have also developed some parameters for PE, PG and Cardiolipin lipids which you might want to have a look at (for comparison with your ongoing parameter development). Details regarding the behaviour of these lipids are in the supporting info of this paper (http://pubs.acs.org/doi/abs/10.1021/jp207013v). Cheers Tom Joakim Jämbeck wrote: Hi Tom, we have parameters for unsaturated tails now as well as for PE lipids ready for use, the manuscript for these have been submitted. PG and PS lipids are on the way and parameters for cholesterol and sphingomyelin are finished now and the manuscript should be finished relatively soon. Best, J On May 22, 2012, at 15:40 , gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org wrote: Date: Tue, 22 May 2012 13:49:48 +0100 From: Thomas Piggot t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk Subject: Re: [gmx-users] forcefields for lipids To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4fbb8b6c.70...@soton.ac.uk mailto:4fbb8b6c.70...@soton.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Joakim, I am interested to know what other lipids this force field has been extended to include. Do you have parameters for unsaturated lipid tails and other classes of phospholipid (such as PE and PG)? Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] forcefields for lipids
Hi, In my opinion the choice of force field will depend upon exactly what you are simulating and why you are simulating it. Different force fields (both lipid and protein) have their own advantages and disadvantages and so it is really up to you to decide this (after doing some background reading about different force fields). Additionally you may wish to use more than one force field to run repeat simulations to verify what you see in your simulations, if this is feasible to do. Cheers Tom Shima Arasteh wrote: I'm going to simulate the protein in POPC bilayer. Do you suggest this forcefield for this kind of bilayer too? Thanks so much for your reply. Sincerely, Shima *From:* Thomas Piggot t.pig...@soton.ac.uk *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, May 22, 2012 10:15 PM *Subject:* Re: [gmx-users] forcefields for lipids Hi Shima, Yes, the phospholipid parameters are available to use. I am currently in the process of uploading them to the Lipidbook website. If you check this website soon they should be available to download (DPPE and POPE parameters and bilayers are already there). For accessing them on Lipidbook the name of the force field is the GROMOS-CKP lipid force field. The parameters are consistent for use with the GROMOS 53A6 and GROMOS 54A7 protein force fields for simulating membrane proteins systems. I should also note that the Kukol DMPC and DPPC parameters (http://pubs.acs.org/doi/abs/10.1021/ct8003468) are also consistent with these phospholipid parameters, if you wish to simulate mixed lipid bilayers. Cheers Tom Shima Arasteh wrote: Is this FF available for others to use? Thanks. Sincerely, Shima *From:* Thomas Piggot t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Tuesday, May 22, 2012 7:39 PM *Subject:* Re: [gmx-users] forcefields for lipids Thanks Joakim, I will be very interested to see how these different lipids behave. This looks like it could be a really useful force field. We have also developed some parameters for PE, PG and Cardiolipin lipids which you might want to have a look at (for comparison with your ongoing parameter development). Details regarding the behaviour of these lipids are in the supporting info of this paper (http://pubs.acs.org/doi/abs/10.1021/jp207013v). Cheers Tom Joakim Jämbeck wrote: Hi Tom, we have parameters for unsaturated tails now as well as for PE lipids ready for use, the manuscript for these have been submitted. PG and PS lipids are on the way and parameters for cholesterol and sphingomyelin are finished now and the manuscript should be finished relatively soon. Best, J On May 22, 2012, at 15:40 , gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org wrote: Date: Tue, 22 May 2012 13:49:48 +0100 From: Thomas Piggot t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk Subject: Re: [gmx-users] forcefields for lipids To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4fbb8b6c.70...@soton.ac.uk mailto:4fbb8b6c.70...@soton.ac.uk mailto:4fbb8b6c.70...@soton.ac.uk mailto:4fbb8b6c.70...@soton.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Joakim, I am interested to know what other lipids this force field has been extended to include. Do you have parameters for unsaturated lipid tails and other classes of phospholipid (such as PE and PG)? Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe
Re: [gmx-users] forcefields for lipids
Hi, In addition to the ones already mentioned (CHARMM, GAFF/AMBER, Berger, OPLS-AA) there are several united-atom GROMOS based lipid forcefields (43A1-S3, 53A6L/54A7, 53A6 Kukol, etc.). The Lipidbook website is a useful place to find lots of lipid parameters in one location: http://lipidbook.bioch.ox.ac.uk/ The choice of force field will depend upon what you wish to simulate. With PC lipids there are more force fields available compared to other phospholipids, so your choice of lipid may dictate your choice of force field. Additionally some of the available lipid force fields may work well for one type of lipid but not another. Finally if you have a membrane-protein system you also need to consider the combination with an appropriate protein force field. Cheers Tom Peter C. Lai wrote: Off the top of my head: There are the Berger lipids for the gromos FFs (Justin's tutorial) There was a B2 Adrenergic receptor paper that used Amber. and of course Martini appears to be everyone's favorite coarse grain FF. The literature search shall be left as an exercise for the reader. (You can even use google to search this mailing list or mirrors of it) On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote: Dear gmx users, Which force fields are suggested for lipids? Except CHARMM, any other forcefields? Anybody may suggest me articles in this about? Thanks in advance Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Best Force Field for a Membrane Protein
Hi, The CHARMM36 force field is already available, see the user contributions section on the GROMACS website. As for the original question on which is best, it is a hard question to answer. It really depends on what you need. For example, are you just looking at PC lipids in your membrane, or do you want to use lipids like PE, PG, etc. This may alter your choice of force field. Also be aware if you use an all-atom force field for your membrane (like CHARMM) your simulation will take substantially longer, but the protein model may be slightly better than one of the united-atom GROMOS force fields. You could also choose the combination of the united-atom Berger force field with an all-atom force field (OPLS or AMBER) for the protein. This seems like an attractive compromise but there has not been a huge amount of work looking at these combinations. You really will have to weigh up these different factors yourself and decide what is best for you. Also be aware that it is really important that once you have made the choice of force field, you use an appropriate set of simulation parameters for this force field. As for your point about the GROMOS 53A6 force field, it is know that this force field can have problems with short helices unwinding and there has been an update of this force field (GROMOS 54A7) to try and address these problems. We have been using this force field with no such issues. You can download the force field files from the ATB website (http://compbio.biosci.uq.edu.au/atb/). This might be the simplest solution for you, as you will not need to change your structure file (so no need to re-insert your protein into the membrane). Cheers Tom francesco oteri wrote: Hi Anirban, as far as I know the best force-field for membrane protein system is Charm36: it uses Charm27 for proteins but an improved parametrization for membrane lipids. I don't know if the lipids part has been already ported in gromacs format, but is a trivial task you can do in 1-2 days. Francesco Il giorno 19 aprile 2012 08:32, Anirban Ghosh reach.anirban.gh...@gmail.com mailto:reach.anirban.gh...@gmail.com ha scritto: Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Ion parameters in OPLS AA force field
Hi Florian, I believe the ion parameters are the Aaqvist parameters: http://pubs.acs.org/doi/abs/10.1021/j100384a009 Cheers Tom Dommert Florian wrote: Hello, there are several ion non-bonded ion parameters provided in the OPLS-AA files of Gromacs, and the reference from an article Jorgensen et al. from 2001. However I was not able to find the corresponding atom types in this article and so far also not in any other article of the OPLS-AA authors. Does anyone have an idea where these parameters come from ? /Flo -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Literature reading on DispCorr for energy and pressure
Hi, This paper comes to mind: Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations Shirts, Mobley, Chodera and Pande J. Phys. Chem. B 2007, 111, 13052-13063 Cheers Tom Andrew DeYoung wrote: Hi, Only if you have time, can you please recommend literature reading on how long-range dispersion corrections are computed? I have been using DispCorr = EnerPres for my simulations, which are in the NPT ensemble. When I search through this user's list, I find frequent mention of the fact that DispCorr = EnerPres is useful for obtaining the correct system density at the end of an NPT simulation. I have the general idea that dispersion correction corrects for the cut-off of the Lennard-Jones potential ( for example, http://lists.gromacs.org/pipermail/gmx-users/2003-August/006717.html ), which is always attractive at long range. Perhaps this is (very roughly, very qualitatively) analogous to the Ewald summation, which is a sort of electrostatic correction to correct for the cut-off of the Coulomb interaction? However, I would be interested in more details about how this correction to the Lennard-Jones potential is accomplished, and what approximations it introduces and assumptions it makes. Section 4.8 of the manual gives many details, but I am curious if you can recommend any review-type articles about this correction. Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] forcefield.itp file for gromos45a3 and oplsaa
Hi, In the GROMOS force fields the non-bonded interactions are explicitly given as some atom types have more than one C12 value. The different C12 values are used for interactions with different atom types. This means you need to be very careful when modifying the ffnonbonded.itp for the GROMOS force fields. If you wish to do this I suggest that you read of the GROMOS 53A6 force field paper (DOI: 10.1002/jcc.20090). Cheers Tom On 04/01/12 06:18, Mark Abraham wrote: On 4/01/2012 4:43 PM, XUEMING TANG wrote: Hello I am trying to adjust compound LJ parameter in oplsaa (sigmaepsilon) and also in Gromos (C6 and C12) forcefield for comparison. The original ffnonbonded.itp file in oplsaa.ff has no pair potential listed. While the original ffnonbonded.itp file in gromos**.ff listed all the pair potentials. If I change one atom potential, do I need to do anything to generate the new pair potential before running a simulation in opls-aa force field? Or how to generate the pair potentials? While for the case of gromos forcefield, the forcefield.itp file shows no pair potential will be generated. Is there any automatic ways to generate the modified LJ potentials? Should I list every possible LJ pair potentials in nonbonded.itp file? It looks like some very tedious work if several atoms are going to be modified. Also, what does fudge LJ and fudgeQQ mean in forcefield.itp file? Values of those two are different for OPLS and Gromos. In general, two force fields work differently and have their own idiosyncrasies that will show up in how GROMACS implements them. When modifying them, you should be sure to check the original literature and the GROMACS manual and satisfy yourself how your changes will work. You should search the manual for discussion of the use of gen-pairs and the fudge values. I don't know why the list of [ nonbond_param ] values is exhaustive - you'd think the combination rules could be used. In practice, you only need to add parameters for interactions that can occur in your system, and grompp will complain about those that it can't find. Mark -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Parametrisation of the heteroatomic pdb
Hi James, I suggest to see the differences in topologies for L and D amino acids (in the GROMOS force fields at least) you look in the aminoacids.rtp file and in particular the differences between the ALA and DALA entries. Cheers Tom James Starlight wrote: Mark, I've mistaken I need to invert impropers for DIHEDRAL for Calpha atom. By this way I want to change L form to D form for Gromos ff. Does this correct ? [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 NCACBCG gd_34 NCA C+N gd_40 CACBCG CD1 gd_34 So I think that I need to make corrections in that gd_n files. But in what exactly and where in manual could I read about that parametrisation ? It could be cool that in that section such information present :) http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral 2011/11/10 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au First, identify that there's anything to invert. Look at the #define lines for gi_1 and gi_2 and the manual sections for impropers. There's nothing associated with any handedness. The impropers for chirality prevent inversion, rather than enforcing a particular chirality. You can test this yourself. Make a .tpr of an L-amino acid and .gro files of each chirality, and then use mdrun -rerun Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s Lconfiguration. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] source of opls Mg2+ parameters?
Hi Chris, If I remember correctly the magnesium ion parameters are the Aquvist parameters (http://pubs.acs.org/doi/abs/10.1021/j100384a009). Cheers Tom chris.ne...@utoronto.ca wrote: Dear users: does anybody know where the OPLS magnesium parameters are from? As far as I can tell, they are not in Jorgensen 1996 or Kaminski 2001, In spite of the fact that many simulation studies reference these papers for their magnesium opls parameters. In fact, I do not think that the opls mg2+ parameters in ions.itp are taken from any of the references listed in ffoplsaa.itp. I checked the following references with searches for magnesium, mg2+, and a general visual scan: ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, ; J. Am. Chem. Soc. 118, 11225-11236 (1996). ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998). ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998). ; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999). ; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001). ; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001). ; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J. Phys. Chem. B 105, 6474 (2001). From a web search, the TINKER program indicates that it uses OPLS Mg2+ parameters from an unpublished source: OPLS All-Atom Parameters for Organic Molecules, Ions, Peptides Nucleic Acids, July 2008 as provided by W. L. Jorgensen, Yale University during June 2009. These parameters are taken from those distributed with BOSS Version 4.8. (above quote from http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm ) although those tinker parameters (sigma=0.1450 and epsilon=3.9600) do not match the values for opls in the gromacs ions.itp (sigma=0.164447 and epsilon=3.66118). I did not check out BOSS directly (it costs money), but I did look at the manual on the Jorgensen web page, although that manual does not contain Mg2+ parameters. I also checked the gromos magnesium parameters that are distributed with gromacs and verified that these c6/c12 values do not match the sigma/epsilon opls values after a conversion with g_sigeps. Thank you very much for your time and assistance, Chris. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charmm27 ff for membrane protein simulation
By default in the CHARMM27 force field files there is no DPPC, as this is made up from a combination of other entries in the rtp file (because this is the way it is done in the CHARMM program's files). If you wish to use DPPC you can construct yourself a complete DPPC rtp entry. To do this you it is probably easiest to duplicate the DMPC entry and add the corresponding atoms and bonds for two extra carbons in each tail. Alternatively you could use the CHARMM36 force field (available to download from the contributions section of the website), there should already be an entry for DPPC. Cheers Tom On 18/10/11 19:45, Justin A. Lemkul wrote: James Starlight wrote: Greetings! Recently I've found that Charmm27 ff is widely used for the simulation of the membrane proteins. I've tried to work with pure DPPC bilayer in pdb2grx and obtain that charm27 ff included in the Gromacs is lack for the parametries for the lipids. Could you tell me where I could obtain those parametries ( and tutorial of how it might be included in processing of lipids) or full functional charmm27 ff that already has pre-built those parametries? Most of the common lipids are already present in lipids.rtp in charmm27.ff in Gromacs 4.5.x; if you are looking for lipids not present there, please be more specific as to what you need. The only membrane protein tutorial to my knowledge is my own. Dealing with CHARMM should be significantly easier, however, as no modification of the force field is necessary. Run pdb2gmx on a single lipid molecule, convert the .top to .itp (see the wiki) and #include it in the .top for your protein, just like in my tutorial. -Justin Thank you for help James -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topologies for POPE and DMPE
Hi Roy, PE lipids are less frequently used than PC ones and there are fewer topologies available. Also it has been shown that using the Berger PC lipid topologies (the most frequently used united-atom PC lipids) and simply changing the CH3 atoms in the head group to H is not a good approach for PE (de Vries et al. DOI: 10.1021/jp0366926 is I think the first mention of this). Other PE topologies I am aware of are either the all-atom CHARMM (27 or 36) lipids or there are two united-atom GROMOS PE topologies: The first is the GROMOS43A1-S3 force field which has a POPE topology (you can download this from the contributions section on the GROMACS website). I have simulated a POPE membrane using these parameters before with no problems. The second (and here is a shameless plug for some of my work, sorry!) is a GROMOS53A6 based PE described in a paper we have just got accepted into J. Phys. Chem B (http://dx.doi.org/10.1021/jp207013v). The supplementary information for this paper (which is not yet available) has an analysis/validation of POPE and DPPE membrane using these parameters which are based upon the PC topologies of Kukol (DOI: 10.1021/ct8003468) and Chandrasekhar (DOI: 10.1007/s00249-002-0269-4). If you (or anyone else) wish to use these PE topologies send me an email off-list and I can let you have them. I have not tested DMPE yet but I would imagine it should be similar to DPPE and you can also make a DMPE bilayer from a DPPE one by simply removing two CH2 groups from each lipid tail and equilibrating the new membrane. Cheers Tom Roy Lee wrote: Dear all, I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4, and a forcefield of gromos96. However i don't have the topologies files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Any help is much appreciated. Thanks a lot! Roy -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topologies for POPE and DMPE
Hi Pramod, Please keep all general queries and questions on the GROMACS mailing list. For CHARMM27, POPC can be found as an rtp entry. This means a topology can be generated using pdb2gmx. It is easiest if you do this using one POPC lipid and then make an itp from the top. A CHARMM POPC bilayer can be downloaded from the internet (http://terpconnect.umd.edu/~jbklauda/research/download.html). Cheers Tom ram bio wrote: Dear Dr.Tom, This is in response to the your message regarding the lipid bilayers for MD simulation. I have a protein and ligand complex to be simulated in lipid bilayer. Do, you have POPC structure and itp files parameterised by CHARMM 27 FF. Regards, Pramod On Mon, Oct 17, 2011 at 12:07 PM, Thomas Piggot t.pig...@soton.ac.uk wrote: Hi Roy, PE lipids are less frequently used than PC ones and there are fewer topologies available. Also it has been shown that using the Berger PC lipid topologies (the most frequently used united-atom PC lipids) and simply changing the CH3 atoms in the head group to H is not a good approach for PE (de Vries et al. DOI: 10.1021/jp0366926 is I think the first mention of this). Other PE topologies I am aware of are either the all-atom CHARMM (27 or 36) lipids or there are two united-atom GROMOS PE topologies: The first is the GROMOS43A1-S3 force field which has a POPE topology (you can download this from the contributions section on the GROMACS website). I have simulated a POPE membrane using these parameters before with no problems. The second (and here is a shameless plug for some of my work, sorry!) is a GROMOS53A6 based PE described in a paper we have just got accepted into J. Phys. Chem B (http://dx.doi.org/10.1021/jp207013v). The supplementary information for this paper (which is not yet available) has an analysis/validation of POPE and DPPE membrane using these parameters which are based upon the PC topologies of Kukol (DOI: 10.1021/ct8003468) and Chandrasekhar (DOI: 10.1007/s00249-002-0269-4). If you (or anyone else) wish to use these PE topologies send me an email off-list and I can let you have them. I have not tested DMPE yet but I would imagine it should be similar to DPPE and you can also make a DMPE bilayer from a DPPE one by simply removing two CH2 groups from each lipid tail and equilibrating the new membrane. Cheers Tom Roy Lee wrote: Dear all, I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4, and a forcefield of gromos96. However i don't have the topologies files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Any help is much appreciated. Thanks a lot! Roy -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM 36 force field
Hi Giovanni, Rather than me just provide you with an mdp file I would suggest that you go through the Klauda paper with a copy of the online GROMACS mdp options open (http://manual.gromacs.org/online/mdp_opt.html). This way you should be able to work out what the appropriate setting are yourself using this online help. This should be far more useful for you in the long term. Of course I am happy to answer any specific questions you have about the choices that are still unclear to you after you have tried this (although most should be pretty clear I think). Or, if you have already done this and you are still unsure about an mdp option you will have to be more specific in your question. Cheers Tom Giovanni Mancini wrote: Dear Tom, Thank you very much for your answer. I am aware of the paper you suggested but it is not clear for all mdp parameters. My intent is the simulation of a small organic molecule into the DPPC membrane making use of the CHARMM36 force field. There are significant differences when I change some mdp parameters, according to the advice from the gmx-user list. If there is a checked set of the above parameters that are really work with the NPT ensemble, may I have access to it? Best regards Giovanni -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 force field
Hi Giovanni, Yes it can, but the behaviour of the membrane can be quite dependent on the simulation parameters used. Check out this the mailing list archives for more details about this. I would advise using the simulation parameters as used in the CHARMM36 paper of Klauda et al. and you should be fine. Cheers Tom Giovanni Mancini wrote: Dear GROMACS users, I am interested in simulating a DPPC membrane with CHARMM 36 force field in GROMACS. The charmm36.ff_4.5.4.tgz was downloaded by the following web page: http://www.gromacs.org/Downloads/User_contributions/Force_fields. When the membrane is simulated in NPz(A=0.64nm^2)T ensemble all goes fine but if I turned to NPT ensemble (P=1bar in z direction and 1bar for the lateral pressure) the area per lipid reduces significantly. My question is whether the CHARMM36 force field can be employed with the NPT ensemble? Best regards Giovanni -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MARTINI / all-atom mapping
Hi Mike, If you download the rev_trans.tar.gz archive from the reverse transformation tutorial on the Martini website (http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation) the mapping section at the end of the dppc.itp file provides the details of the mapping for this lipid. Cheers Tom On 30/08/11 18:57, Michael Daily wrote: Xavier, I did find the atom2cg.awk script on the downloads- tools of the martini website, but there is no corresponding one for lipids. In any case I can probably figure out the mapping by trial and error, just based on inter-bead distances, but it would be nice to have it officially documented. Mike On Tue, Aug 30, 2011 at 3:06 AM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: it must be some example of mapping lipids on the website: cgmartini.nl http://cgmartini.nl On Aug 30, 2011, at 3:55 AM, Michael Daily wrote: Hi all, I am trying to reverse-map some martini lipids to united atom. In order to do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping. I cannot find this, only an imprecise graphic, in the MARTINI paper; the martini.itp file doesn't appear to list which heavy atoms are represented by each CG bead either. For example, I'm looking for something like: 'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'], 'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'], 'GL1' : ['C13', 'O14', 'C15', 'O16'], 'GL2' : ['C32', 'O33', 'C34', 'O35'], etc. For some atoms it's obvious which MARTINI groups they belong in, but others on the borderline are not obvious. For example, does C12 belong in PO4 or GL1? Anybody have a master list like this? Thanks, Mike -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 tel:509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error from residues added to rtp file
Hi, I think the problem is that you have a dash rather than a minus symbol for the sign of the charge on the OD atom. Cheers Tom Delmotte, Antoine wrote: Dear Gromacs users, I am currently trying to run an MD simulation with the OPLS-AA force field on a protein having different non standard residues and a ligand. I found the charges for the OPLS force field for these residues in the literature and I am now trying to add them in the OPLS force field parameter files. I have edited the aminoacids.rtp and the aminoacids.hdb files for the OPLS-AA force field, as well as the residuetypes.dat file. Here is an example for one of the amino acids, hydroxyproline: [ HYP ] [ atoms ] N opls_239 -0.140 1 CA opls_246 0.010 1 HA opls_140 0.060 1 CB opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_137 -0.120 3 HG1 opls_140 0.060 3 OD opls_167 −0.683 3 HD opls_168 0.743 3 CD opls_245 -0.050 4 HD1 opls_140 0.060 4 HD2 opls_140 0.060 4 C opls_235 0.500 5 O opls_236 -0.500 5 [ bonds ] N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG OD OD HD CG CD CD HD1 CD HD2 CD N C O -C N [ impropers ] -C CA N CD improper_Z_N_X_Y CA +N C O improper_O_C_X_Y When I run pdb2gmx, I get the following error, which is not very informative: All occupancies are one Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residue 58 --- Program g_pdb2gmx, VERSION 4.5.3 Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/kernel/resall.c, line: 389 Fatal error: in .rtp file in residue HYP at line: OD opls_167 −0.683 3 I would be grateful if anyone could shed some light on the origin of this error, and on what I can do to correct it. I am using Gromacs 4.5.3. Thanks a lot in advance, Antoine -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charge groups in Charmm for lipids
The new GROMACS 4.5.4 version of the CHARMM36 force field files are now uploaded on the GROMACS website contributions section. Just to note that if anyone downloaded the 4.5.4 version uploaded a few hours ago then the atomtypes.atp file was incomplete and should download this new version. Sorry for any problems caused by this. Cheers Tom On 06/08/11 02:28, Thomas Piggot wrote: Sure, I will upload a GROMACS 4.5.4 version of the force field files to the website. Cheers Tom On 06/08/11 01:34, Peter C. Lai wrote: On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS. Check out the mailing list archives for more details about this. On another note you might like to take a look at the contributed CHARMM36 force field (available to download on the GROMACS website). There is a DPPG entry in the lipids.rtp file that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Just as an aside, can you update your C36 with the C27 files for proteins and nucleic acids? That saves us from having to copy the charmm27.ff files for those compounds into charmm36.ff...(since the amino and nucleic acid topologies in charmm36.ff still use nondistinct chargegroups requiring the use of -nochargegrp to pdb2gmx) Thanks -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charge groups in Charmm for lipids
Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS. Check out the mailing list archives for more details about this. On another note you might like to take a look at the contributed CHARMM36 force field (available to download on the GROMACS website). There is a DPPG entry in the lipids.rtp file that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Cheers Tom On 06/08/11 00:22, Michael McGovern wrote: Hi, I'm making a lipid topology for DPPG in the charmm forcefield in gromacs 4.5. I'm putting it together from pieces of what already exists as suggested in the charmm files. I noticed that there are charge groups in the original charmm files, and these were reflected in the gromacs topology in the 4.5 beta release, but in 4.5.3 and 4.5.4, every atom has its own charge group. So for instace, POPC in the beta release had a topology that began: [ POPC ] [ atoms ] N NTL -0.60 0 C11 CTL2-0.10 0 C12 CTL5-0.35 0 C13 CTL5-0.35 0 C14 CTL5-0.35 0 H11 HL 0.250 H12 HL 0.250 H21 HL 0.250 H22 HL 0.250 H23 HL 0.250 H31 HL 0.250 H32 HL 0.250 H33 HL 0.250 H41 HL 0.250 H42 HL 0.250 H43 HL 0.250 C15 CTL2-0.08 1 H51 HAL20.091 H52 HAL20.091 P1 PL 1.502 O3 O2L -0.78 2 O4 O2L -0.78 2 O1 OSL -0.57 2 O2 OSL -0.57 2 C1 CTL2-0.08 3 ... While in 4.5.4 this is [ POPC ] [ atoms ] N NTL -0.60 0 C11 CTL2-0.10 1 C12 CTL5-0.35 2 C13 CTL5-0.35 3 C14 CTL5-0.35 4 H11 HL 0.255 H12 HL 0.256 H21 HL 0.257 H22 HL 0.258 H23 HL 0.259 H31 HL 0.2510 H32 HL 0.2511 H33 HL 0.2512 H41 HL 0.2513 H42 HL 0.2514 H43 HL 0.2515 C15 CTL2-0.08 16 H51 HAL20.0917 ... The charge groups do not have integer charge and are all one atom. The beta version has groups that agree with the charmm groups and have integer charge. Was this changed on purpose? The beta version seems correct to me, but am I missing something as to why this change would be made? Thanks -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charge groups in Charmm for lipids
Sure, I will upload a GROMACS 4.5.4 version of the force field files to the website. Cheers Tom On 06/08/11 01:34, Peter C. Lai wrote: On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS. Check out the mailing list archives for more details about this. On another note you might like to take a look at the contributed CHARMM36 force field (available to download on the GROMACS website). There is a DPPG entry in the lipids.rtp file that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Just as an aside, can you update your C36 with the C27 files for proteins and nucleic acids? That saves us from having to copy the charmm27.ff files for those compounds into charmm36.ff...(since the amino and nucleic acid topologies in charmm36.ff still use nondistinct chargegroups requiring the use of -nochargegrp to pdb2gmx) Thanks -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC
Hi Igor, Thanks for the reply but I think you slightly missed the point I was trying to make. I followed the approach you mention for the double bond and (with the two force fields I tried) got the values I discussed in my last email, which when compared to the published values seem to be incorrect. Just to confirm, my index file (for the unsaturated calculation) contains (below is just pasted from make_ndx): For CHARMM36: 0 C28 :72 atoms 1 C29 :72 atoms 2 C210:72 atoms 3 C211:72 atoms and for GROMOS53A6L: 0 C1H : 128 atoms 1 C1I : 128 atoms 2 C1J : 128 atoms 3 C1K : 128 atoms My command for g_order (this is just for CHARMM36 but I use the same command for GROMOS53A6L on different files) is: g_order_4.5.4 -s for-md-popc-charmm36.tpr -f md-popc-charmm36.xtc -n chain2_unsat.ndx -od deut_chain2_unsat.xvg -unsat If anyone can see what might be going wrong then any help would be greatly appreciated. Cheers Tom Igor Marques wrote: thomas, i've recently placed a similar question and justin asked me to show my index for the double bound calculation, so, i'm asking you the same. you should have Ci-1 Ci - the first carbon of the double bound Ci+1 - the second carbon of the double bound Ci+2 in that index doing this, for C9 and C10 i've obtained the following values 0.0738068 -0.000533683 that you should then replace in the correct positions in the sn2 output good luck, and sorry if i'm missing the point :| igor Igor Marques On Wed, Jun 8, 2011 at 5:53 PM, Thomas Piggot t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk wrote: Hi Everyone, I am facing a problem when calculating the lipid deuterium order parameters for the unsaturated carbons of the sn-2 tail of POPC using g_order with GROMACS version 4.5.4 (although I have tried other older versions too but they all give the same results). Firstly, I should say the the calculation of the order parameters for the saturated sn-1 chain (and also both chains of DPPC) behave as I would expect, and produce order parameters that compare well to previously published simulations and experimental values. To calculate the order parameters of the unsaturated chain I am following the approach as given on the GROMACS website (http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order), so splitting the calculation into two parts for the saturated and unsaturated regions of the chain. The problem I am facing is that the order parameter for carbon 9 (so the first carbon in the double bond), calculated using the -unsat option, is much larger than expected. By this I mean that for the two different force fields I have tested (namely the CHARMM36 parameters of Klauda et al., and the GROMOS 53A6L parameters of Poger et al.) the order parameter for this carbon is much larger than the published simulation values and also much larger than experimental values. To highlight this, I have just put the numbers I have obtained using g_order for this carbon below, and compared to some rough values I have estimated from figures provided in the Klauda and Poger papers: CHARMM36 g_order:0.133732 Klauda estimate:0.06 GROMOS53A6L: g_order:0.199651 Poger estimate: 0.07 Myself and a colleague have tried looking into the code to determine how the order parameters are calculated using the -unsat option, however we couldn't quite follow the calculation. Hopefully someone who knows something more about g_order can help with this problem. Again I should stress that it appears that the main difference in order parameters between what I have calculated and the published ones is just in this one carbon, for both force fields. A similar issue to this has also been reported previously on the list for this carbon of POPC using the 'Berger' force field (http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html). Thank you for any help anyone can give Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx
Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC
Hi, Both the trajectories are 100 ns in length (plus I have a repeat of each simulation using different starting velocities). The results from a block analysis, and analysis of the repeat simulations, give almost identical results to those in my previous message. The other thing is that the remainder of the order parameters also give sensible numbers, both for the saturated carbons in the rest of the oleoyl chain and in the palmitoyl chain. Regarding the mdp settings, then I used the same parameters as given in the papers from which I quoted the previous values. For CHARMM36, this includes a 1 fs timestep, the CHARMM TIP3P water (tips3p), constraints = hbonds and a switching of the vdW interactions between 0.8-1.2 A. For the GROMOS53A6L simulations then this is with a cut-off for the electrostatic interactions of 1.4 nm and a reaction-field correction applied beyond the cut-off, a vdW cut-off of 1.4 nm, rlist of 0.8, nstlist every 5 steps, a 2 fs time step and the SPC water model. I can provide full mdp's if necessary. Analysis of other membrane properties from the simulations (such as area and volume per lipid, area compressibility, electron density) all give comparable results to those previously published for these two force fields. All of this leads me to suspect that there may be a problem in the way g_order calculates the order parameter for the unsaturated carbons, however I am by no means certain of this. Currently we are trying to calculate the order parameters from the all-atom CHARMM36 simulations using a different bit of code, I will report back with the results if we can get this to work. Cheers Tom Justin A. Lemkul wrote: Thomas Piggot wrote: Hi Igor, Thanks for the reply but I think you slightly missed the point I was trying to make. I followed the approach you mention for the double bond and (with the two force fields I tried) got the values I discussed in my last email, which when compared to the published values seem to be incorrect. Just to confirm, my index file (for the unsaturated calculation) contains (below is just pasted from make_ndx): For CHARMM36: 0 C28 :72 atoms 1 C29 :72 atoms 2 C210:72 atoms 3 C211:72 atoms and for GROMOS53A6L: 0 C1H : 128 atoms 1 C1I : 128 atoms 2 C1J : 128 atoms 3 C1K : 128 atoms My command for g_order (this is just for CHARMM36 but I use the same command for GROMOS53A6L on different files) is: g_order_4.5.4 -s for-md-popc-charmm36.tpr -f md-popc-charmm36.xtc -n chain2_unsat.ndx -od deut_chain2_unsat.xvg -unsat If anyone can see what might be going wrong then any help would be greatly appreciated. Are your results converged? From the g_order command, you're considering the whole trajectory. I'd suggest the usual block averaging approach to see if you're converged. There's nothing wrong with the way you're calculating the order parameters, so the only other thing I would suspect (other than lack of convergence) is that the .mdp settings are somehow giving unexpected results. Membrane properties can be very sensitive to vdW and electrostatics methods. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] All-atom topologies for lipid head groups
Hi, A force file like this does exist (http://pubs.acs.org/doi/abs/10.1021/jp800687p) but be aware, like the CHARMM27 force field it is based upon, you will need to use surface-tension to keep these lipids in the correct phase. Cheers Tom Justin A. Lemkul wrote: Ioannis Beis wrote: Dear Gromacs users, I am a new user and I am trying to study the physical properties of the interactions between cytosolic proteins and lipids. I have created the Berger-Gromos combination, as described by Mr. Justin Lemkul in his KALP15 in DPPC tutorial, as well as Berger-OplsAA, as described by Mr. Chris Neale in gromacs mailing list. All-atom topologies might turn out to be crucial in my work, both in the results and the data analysis (e.g. H-bonds). Even if the all-atom model of Opls-AA is used for the proteins, the lipid head groups would still have a united-atom description and therefore the interactions can't be treated in an all-atom level. I thought of creating a new topology for the lipid head groups under a head.itp file, by using parameter values from Dundee server and/or Opls-AA, even though I do not know yet exactly how and I feel very unsure about the eventual incorporation into the Berger-OplsAA combination. Then taking single lipids of pre-equilibrated membranes, editing accordingly the coordinate file (i.e. replacement of polar head atoms and use of new coordinates, names and residue names for them) and subsequently building bilayers. I would really appreciate if someone could send suggestions. In addition, if someone already has an all-atom description of lipid head-groups compatible with a protein-membrane force field combination with all-atom protein description, I would be grateful if he/she could share. Thank you in advance. It sounds to me like you're trying to create a Frankenstein force field. Why wouldn't a UA representation of the lipids work? For hydrogen bonding, all polar groups are represented with explicit H atoms. This is generally true of all UA force fields, for lipids and proteins alike. If you really want an AA representation of your molecules, you're probably better off just applying the CHARMM force field to the whole system. The latest version of Gromacs supports CHARMM, which includes a number of common lipids. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC
Further to my last message we have managed to use a tcl script in VMD to calculate the order parameters for the POPC chains in the CHARMM36 simulation. I have put the values for this calculation and the values I obtained using g_order (over the same period in the same trajectory) below (this is for the sn-2 chain, for the sn-1 chains then the 2 methods produce very similar results). I think this shows that there is a problem with g_order and the calculation of the order parameter parameters for the first carbon in the double bond of the unsaturated tail. carbon g_order VMD script 20.0967924 0.095035 30.2081430.207425 40.2032510.203339 50.2142360.213071 60.1924480.191573 70.18472 0.182894 80.1017350.108403 90.1343630.061669*** 100.0444899 0.049259 110.0703591 0.077746 120.1166840.115886 130.1222370.121924 140.1264240.125857 150.1143840.114213 160.1038680.103317 170.0806387 0.080544 If nobody can see that I have done anything obviously wrong then I will file an issue regarding this on redmine. Cheers Tom Thomas Piggot wrote: Hi, Both the trajectories are 100 ns in length (plus I have a repeat of each simulation using different starting velocities). The results from a block analysis, and analysis of the repeat simulations, give almost identical results to those in my previous message. The other thing is that the remainder of the order parameters also give sensible numbers, both for the saturated carbons in the rest of the oleoyl chain and in the palmitoyl chain. Regarding the mdp settings, then I used the same parameters as given in the papers from which I quoted the previous values. For CHARMM36, this includes a 1 fs timestep, the CHARMM TIP3P water (tips3p), constraints = hbonds and a switching of the vdW interactions between 0.8-1.2 A. For the GROMOS53A6L simulations then this is with a cut-off for the electrostatic interactions of 1.4 nm and a reaction-field correction applied beyond the cut-off, a vdW cut-off of 1.4 nm, rlist of 0.8, nstlist every 5 steps, a 2 fs time step and the SPC water model. I can provide full mdp's if necessary. Analysis of other membrane properties from the simulations (such as area and volume per lipid, area compressibility, electron density) all give comparable results to those previously published for these two force fields. All of this leads me to suspect that there may be a problem in the way g_order calculates the order parameter for the unsaturated carbons, however I am by no means certain of this. Currently we are trying to calculate the order parameters from the all-atom CHARMM36 simulations using a different bit of code, I will report back with the results if we can get this to work. Cheers Tom Justin A. Lemkul wrote: Thomas Piggot wrote: Hi Igor, Thanks for the reply but I think you slightly missed the point I was trying to make. I followed the approach you mention for the double bond and (with the two force fields I tried) got the values I discussed in my last email, which when compared to the published values seem to be incorrect. Just to confirm, my index file (for the unsaturated calculation) contains (below is just pasted from make_ndx): For CHARMM36: 0 C28 :72 atoms 1 C29 :72 atoms 2 C210:72 atoms 3 C211:72 atoms and for GROMOS53A6L: 0 C1H : 128 atoms 1 C1I : 128 atoms 2 C1J : 128 atoms 3 C1K : 128 atoms My command for g_order (this is just for CHARMM36 but I use the same command for GROMOS53A6L on different files) is: g_order_4.5.4 -s for-md-popc-charmm36.tpr -f md-popc-charmm36.xtc -n chain2_unsat.ndx -od deut_chain2_unsat.xvg -unsat If anyone can see what might be going wrong then any help would be greatly appreciated. Are your results converged? From the g_order command, you're considering the whole trajectory. I'd suggest the usual block averaging approach to see if you're converged. There's nothing wrong with the way you're calculating the order parameters, so the only other thing I would suspect (other than lack of convergence) is that the .mdp settings are somehow giving unexpected results. Membrane properties can be very sensitive to vdW and electrostatics methods. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http
[gmx-users] Calculation of unsaturated deuterium order parameters for POPC
Hi Everyone, I am facing a problem when calculating the lipid deuterium order parameters for the unsaturated carbons of the sn-2 tail of POPC using g_order with GROMACS version 4.5.4 (although I have tried other older versions too but they all give the same results). Firstly, I should say the the calculation of the order parameters for the saturated sn-1 chain (and also both chains of DPPC) behave as I would expect, and produce order parameters that compare well to previously published simulations and experimental values. To calculate the order parameters of the unsaturated chain I am following the approach as given on the GROMACS website (http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order), so splitting the calculation into two parts for the saturated and unsaturated regions of the chain. The problem I am facing is that the order parameter for carbon 9 (so the first carbon in the double bond), calculated using the -unsat option, is much larger than expected. By this I mean that for the two different force fields I have tested (namely the CHARMM36 parameters of Klauda et al., and the GROMOS 53A6L parameters of Poger et al.) the order parameter for this carbon is much larger than the published simulation values and also much larger than experimental values. To highlight this, I have just put the numbers I have obtained using g_order for this carbon below, and compared to some rough values I have estimated from figures provided in the Klauda and Poger papers: CHARMM36 g_order:0.133732 Klauda estimate:0.06 GROMOS53A6L: g_order:0.199651 Poger estimate: 0.07 Myself and a colleague have tried looking into the code to determine how the order parameters are calculated using the -unsat option, however we couldn't quite follow the calculation. Hopefully someone who knows something more about g_order can help with this problem. Again I should stress that it appears that the main difference in order parameters between what I have calculated and the published ones is just in this one carbon, for both force fields. A similar issue to this has also been reported previously on the list for this carbon of POPC using the 'Berger' force field (http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html). Thank you for any help anyone can give Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: AW: Re: [gmx-users] where can I download POPC membrane file?
In addition to all the other responses, I just wanted to clear up why there is this difference in names. The POPC structure from the link below still has the atom names of the old CHARMM27 lipids (DPPC is fine). As suggested, a simple script can do the conversion for you. Cheers Tom albert wrote: I know this, but this file cannot be used because the atom name is quite different from gromacs CHARMM36 topol library. At 2011-05-30，Rausch, Felix frau...@ipb-halle.de wrote: Check this link given by another (unknown) mailing list user yesterday (Topic name: *about POPC in Gromacs* )! http://terpconnect.umd.edu/~jbklauda/research/download.html http://terpconnect.umd.edu/%7Ejbklauda/research/download.html *Von:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org im Auftrag von albert *Gesendet:* So 29.05.2011 21:23 *An:* Discussion list for GROMACS users *Betreff:* Re:Re: [gmx-users] where can I download POPC membrane file? But I don't think it is pre-equilibrium POPC membrane.. and more over, the position from VMD is not pre-aligned with OPM database. It would be a great problem for putting our protein in the membrane.. At 2011-05-30，Sergio Manzetti sergio.manze...@vestforsk.no mailto:sergio.manze...@vestforsk.no wrote: You can build it using VMD (VIsual Molecular Dynamics) 2011/5/30 albert leu...@yeah.net mailto:leu...@yeah.net Dear all: I would like to use charmm36 and POPC for membrane protein simulation. and I am wondering where can I download charmm36 pre-pribriumed POPC PDB and topol file for gromacs? Thank you very much Best -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] lipids per area charmm36 popc
I agree with Justin, 1 ns is just nowhere near long enough. Something in the tens of ns should do it. I have used pretty much the same settings as you (using the CHARMM water, as you have) and get APL's matching those published in the Klauda paper. You are correct that you should not use the dispersion correction, this was discussed in their paper. Cheers Tom On 18/05/11 23:20, Justin A. Lemkul wrote: Peter C. Lai wrote: Hello I am trying to equilibrate from scratch a 196 POPC bilayer using Tom's charmm36.ff. My box has a lot of TIPS3P (charmm) waters above and below the membrane with a box size around 8.5x8.5x12.7. My desired end state is to only use the setup for g_membed but I'd also like to get a pristine tall bilayer that might be useful for other things or colleagues. I ran 1ns NPT so far with: dt = 0.002 continuation= yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.2 vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = POPC SOL tau_t = 0.5 0.5 ref_t = 300 300 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 DispCorr= no comm_mode = Linear comm_grps = POPC SOL The metrics look roughly stable: Energy Average Err.Est. RMSD Tot-Drift - Temperature 3000.00018 0.957697 0.000466096 (K) Density 1017.26 0.24 1.5953 1.4803 (kg/m^3) Pressure1.00795 0.06599.5783 -0.0431925 (bar) Box-X 8.58491 0.036 0.0773839 -0.235388 (nm) Box-Y 8.59611 0.036 0.0774849 -0.235696 (nm) Box-Z 12.43570.1 0.216337 0.659896 (nm) My APLs are ~10A^2/lipid above what they should be according to Klauda and experimental (I get 76-77A^2/lipid vs 65-58A^2/lipid). I suppose with TIPS3P water, I could get closer LJ packing if I turned on DispCorr but I thought that you generally left that off in charmm36 bilayer runs... Now, I also could extend for several ns until density/box drift gets smaller, but any other thoughts (yes this is probably a continuation of the CHARMM36 lipid bilayers thread from October (http://www.mail-archive.com/gmx-users@gromacs.org/msg34582.html)? Later in this thread it is suggested that one use TIPS3P (CHARMM TIP3P) water, so start there, although that discussion found that the APL was consistently underestimated, not overestimated, as is your case. 1 ns is not nearly enough to make solid conclusions about membranes. Lipid rotational relaxation is on the order of 5 ns, and translational relaxation about 10 ns. I'd say you need at least 20 ns of simulation to make any real conclusions, with some of that of course discarded as equilibration. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to use Inflategro with different lipid types
Hi, To construct the bilayer I would just take an equilibrated POPC bilayer and then randomly pick lipids to change to POPE (just by a simple renaming of these lipids and the atom names in the headgroup) and DPPC (which would just require deletion of two united-atoms from the sn-2 chains and renaming of the lipids). Then just run for an equilibration on the bilayer to allow the changes to take effect. There are other approaches you could take but I see this as the simplest solution. Cheers Tom Justin A. Lemkul wrote: Ioannis Beis wrote: Dear gromacs users, I am a new user of gromacs. I am currently trying to build a large bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and no protein embedded in it. I have used single lipids from pre-equilibrated bilayers available at Mr. Tieleman's website. The distance of center of mass of neighboring lipids is 1 nm, so there are small areas with overlaps. I was hoping that I would be able to inflate my membrane and have the lipids totally free of overlaps using Inflategro. Subsequently, I was planning to use the shrinking steps to bring the membrane into physiological size. Is this strategy valid in the first place? If not, I kindly ask for an alternative. In case this method can be used, despite To identify the lipid species their actual residue name must be given which is mentioned in the methodology, the form INFLATEGRO bilayer.gro scaling_factor lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat (protein) only allows the use of one lipid type. How is it possible to run perl with all lipid types at once? I have tried performing inflations using one lipid type at a time and they work. [It worths mentioning that the coordinates of the rest two (uninflated) lipid types slightly change without equilibration (I assume this has to do with Inflategro trying to force the molecules avoid overlaps)]. But I can't treat my membrane as a system that way. I have read the publication introducing the methodology, but it didn't help me solve my problem. I would be grateful if someone could help, also taking into account that I am inexperienced. If you want to use InflateGRO, then you'll have to modify the code to do so. It handles only one lipid type. The alternative is to use normal MD simulations to pack the membrane. On such approach (just thinking out loud here, so it may not work) might be to simulate your membrane (maybe without water) with some external pressure applied to the x-y plane to compress the lipids together. You may need position restraints on, i.e., the lipid headgroups in the z-dimension only during this procedure so the lipids do not simply slam into one another and distort the membrane. Once you've achieved a reasonable membrane, solvate and equilibrate for a longer period of time in the presence of solvent and absence of any restraints. -Justin Kindest regards, Yiannis -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs
Yes, Mark is exactly correct about the glitch. I had just forgotten to change this default charge in the ffnonbonded.itp when copying from another atom. As mentioned this has no impact as these charges are never used by pdb2gmx. Cheers Tom Mark Abraham wrote: On 6/04/2011 2:51 PM, Peter C. Lai wrote: Hello I am constructing a ligand for which I wish to use the new Charmm CGenFF parameters (a long aliphatic ketone). I am using Tom/Par's charmm36 lipid conversion as a baseline template for comparison: For reference, c36 lipid CTL3 atoms (in the case of POPC) map to CG331 in CGenFF; they are both to represent alkane CH3 carbons. Same with CTL2 - CG321. In my case I am particularly interested in CGenFF's parameterization of a ketone carbonyl and oxygen: CG2O5 and OG2D3 (without any associated carboxylic bias or bias from non-carbons found in other parameters. For example C=O in amino acid backbone appears in ffbonded.itp as 5.188e+05 for kB whereas Mark's script yielded a kB of 5.858e+05 for CG2O5=OG2D3, not to mention the bond angles should be different and especially the nonbonded interactions since we've replaced N with C and we have an extra H etc. etc.). My ligand for now is pretty simple: OG2D3 || CG331-CG321-...-CG321-CG2O5-CG331 or, in c36 lipid/prot terms: O || CTL3-CTL2-...-CTL2-C-C-CTL3 How would I convert the relevant atoms in CGenFF's prm file to both dihedral and nonbonded interaction .itp for gromacs? The standard CHARMM .prm files give an indication of how the parameters will be used, so it's just a matter of converting units and taking care of any constants. I tried using Mark's perl scripts and it is giving me wrong LJ terms as well as not picking up any 1,4 interactions (not to mention it has no knowledge of Par's functype 9 for converting Charmm dihderals - we should no longer be using R-B functions). This script predates dihedral functype 9, and implements a post-processing approach to deal with LJ, 1-4 and some dihedrals. I assume you haven't done the latter. In any case, the form of my solutions do not mesh at all with Par's solutions - forget about my scripts. You seem to be only interested in about two atom types, so I'd expect you can convert all the relevant things by hand in under an hour. Finally, a slightly (un)related question: in ffnonbonded.itp, why does CTL2 get a charge of 0.05 when in reality we usually give it -0.18 for associated molecules in the rtp? Is there something I'm missing there? (CTL3 has -0.27 in both the itp and rtp files which makes sense to me). Sounds like a glitch when the file was written - I guess some other carbon also has 0.05 and this was copied and pasted. In any case, the charges in ffnonbonded.itp are never used by pdb2gmx, because precedence-taking residue-specific charges are defined in the .rtp. If one were to use some other tool for generating topologies, I don't know whether charges missing from a [moleculetype] definition are looked up in ffnonbonded.itp. Mark -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: change in the secondary structure after simulation
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
Re: [gmx-users] grompp charge group radii larger than rlist
I think this is because (if I remember correctly) in the downloaded DPPC bilayer from Peter Tieleman's website the lipids have not been made whole again and so are split across the periodic boundaries. If you run a minimisation (so set -maxwarn to 1 during grompp) and re-run grompp on the minimised structure you should see that this problem disappears. Cheers Tom Dr. Ramón Garduño-Juárez wrote: Dear All: I am going through the Justin Lemku tutorial for KALP15 in DPPC. I have reached step three, when I try to generate a trp file for DPPC only by means of : grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I get the following warning: WARNING 1 [file minim.mdp]: The sum of the two largest charge group radii (10.651017) is larger than rlist (1.20) which causes grompp to be terminated. Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. I do not know if I should ignore this warning and use -maxwarn, or if I must modify the mdp file. By the way, I have assigned values from 1.0 to 1.4 to rlist, rcoulomb and rvdw, but I get the same warning all the time... Any idea as to what causes this problem? Much obliged for your help. Cheers, Ramon -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] N-acetyl-d-glucosamine parameters
You could use GLYCAM for the N-acetyl-d-glucosamine with an AMBER force field (probably 99SB or 99SB-ILDN) for the protein. I have never used GLYCAM parameters in GROMACS but I think it should be fairly easy to do using one of the ACPYPE or amb2gmx.pl tools. Cheers Tom Renato Freitas wrote: Hi all! I want to do a simulation of a protein that have a disaccharide (formed by two units of the N-acetyl-d-glucosamine) covalently bonded to the L-asparagine amido group of the protein. Is there an adequate force field in gromacs for dealing with N-acetyl-d-glucosamine? Any help would be appreciated, Thanks Renato -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] galactose bond stretch
I have added an issue on redmine. Cheers Tom Justin A. Lemkul wrote: Thomas Piggot wrote: Whilst this 'problem' you are seeing is probably as Justin has described (a periodic boundary visualisation effect), you should also beware when performing carbohydrate/sugar simulations with the default parameters in the force field files. If I were you I would check the entries against the published parameters (so Lins et al. if you wish to use the 45A4 sugar parameters). From my experience then there are some mistakes in the parameters in the force field files. If this is still the case in the latest release, please file an issue on redmine so that it can be fixed. -Justin Cheers Tom nishap.pa...@utoronto.ca wrote: Thanks Justin! I am using constraints, but like you said it could be just PBC. I did compare some of my calculations to experimental values and they are fairly similar. Nisha P Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I ran a simulation of one molecule of galactose (cyclic) in water. After the simulation run, when I checked the trajectory file in VMD, the bonds in the galactose molecule stretched and during the run changed back to its original starting form. I am using GROMOS force field ffG53A6 and parameters as mentioned for carbohydrates in the forcefield, so I am not sure what went wrong.I generated topology using 'pdb2gmx' command. Also GROMACS did not give any warning during the run and my simulation did not crash. Any insights? You can check bond length distributions with g_bond. Are you using constraints? Are you sure this isn't just a periodicity artifact during visualization? If the bonds deviated severely from equilibrium values or constraint lengths, the simulation would have crashed, so I suspect that what you're seeing is just PBC. -Justin Thanks. Nisha P -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:Re: Which FF could be used for protein-RNA MD simulation in GROMACS?
Hi Stephan, The GROMOS DNA and RNA parameters can be found in the 53A6 rtp file. This file also has some sugar/carbohydrate parameters (which, however, do not seem to accurately match the 45A4 carbohydrate parameters published by Lins et al.) and also an entry for DPPC (although there are plenty of better united-atom lipid parameters available to download from the internet). Whether or not these DNA/RNA parameters should be used ahead of AMBER or CHARMM DNA/RNA parameters is another question and I would say depends on what is being simulated and why. Cheers Tom lloyd riggs wrote: - Message: 1 Date: Thu, 9 Dec 2010 23:16:21 -0500 From: Vitaly Chaban vvcha...@gmail.com Subject: [gmx-users] Re: Which FF could be used for protein-RNA MD simulation in GROMACS? To: gmx-users@gromacs.org Message-ID: aanlktik995o98r7gm8-klac0xuf9m3rb_43+31afa...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hey, Shiyong - I believe your problem is related to X2TOP usage rather than to a proper force field choice. I'd suggest to start with looking into N2T files for the below entries. Cheers. -- Dr. Vitaly V. Chaban Rochester, U.S.A. I just tried G53a6 for protein-RNA simulation. But fatal error shows up. Opening library file /usr/share/gromacs/top//FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges Best -- Shiyong Liu -- Dear Shiyong Liu, I have run across RNA/DNA .itp/.rtp files by searching (for a while) on the internet, a year or so back, which are/were compatable with the G53a6 FF. Aside from that though, I don't remember which lab/site had them. The same is true for lipid and carbohydrate .itp/.rtp libraries. Stephan Watkins -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CMAP error
This is a completely separate issue where the CHARMM force field files from which the GROMACS CHARMM27 rtp entries were created do not have a DPPC entry, rather DPPC in CHARMM is created from using two residues (PALM and PCGL) and two patches (EST1 and EST2). It should have been easy enough to make a CHARMM27 DPPC rtp entry anyway. Cheers Tom Amit Choubey wrote: This may not be related but it was not straight forward to do DPPC membrane simulation using CHARMM FF in gromacs. The DPPC molecule was not defined at all in the FF files. The DPPC is defined in terms of two more residues in CHARMM. amit On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jon Mujika wrote: Dear all, I am setting up a system with GROMACS 4.5.3 and the CHARMM force field. In the protein, I have a neutral lysine, for which CHARMM force filed has a specific residue type (LSN). When I wrote LSN as residue name in the initial pdb file, the topology file was perfectly created by pdb2gmx. However, in the next step, grompp complained about the CMAP torsion between the two previous residues: Fatal error: Unknown cmap torsion between atoms 2747 2749 2751 2754 2757 However, if the LYS residue was written in the initial pdb file and the -lys option included with pdb2gmx (chosen the neutral protonation state for this lysine), grompp did not complain. The problem is that there is a deprotonated tyrosine (bound to a metal) in my system. I created a new residue type, but again the grompp complained about the CMAP between the two previous residues. Unfortunately, in this case I can't fit the problem with any of the pdb2gms options. I think the problem arises when a non-standard residue is included in the initial pdb file. Does someone else find this problem? I would appreciate any advise about how to solve it. I can't promise a solution, but you could try adding LSN and whatever other non-standard residues you need to use in residuetypes.dat. I noticed that LSN is not there, which seems like an omission, since the other CHARMM-specific residue names are there. When LYS is present, probably pdb2gmx is correctly interpreting the residue as protein before converting its name. In the case of LSN or any other non-standard residue, this may not be the case. Check the output of pdb2gmx carefully for any messages that might indicate that a residue of type Other was detected. I've had this cause other problems. If adding LSN to residuetypes.dat fixes the problem, I will file a bugzilla. -Justin Thanks in advance Jon -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dna, lipid simulation
I would tend to agree with Justin rather than Itamar. The GROMOS DNA parameters are not especially good (see http://www.ncbi.nlm.nih.gov/pubmed/20614923) but it depends on what you are wanting to look at. Another option (rather than CHARMM, which for what it is worth is the force field I would probably use) is you could use one of the AMBER forcefields for the DNA and the GAFF lipids (although I forget if there is DPPC available or not, I think the only fully saturated lipid already available might be DMPC), but keep in mind you need to use surface tension with these lipids. As I said the choice really depends on what you want to look at, so some reading of the literature and also seeing what other people have done for similar simulations should help. Cheers Tom On 05/12/10 12:42, Itamar Kass (Med) wrote: Hi Amit, The GROMOS force field had both DNA and lipids parameters, hence you can use it in your simulations. Moreover, there are new lipids parameters by David Poger and Alan Mark which I should give better results compared to the old set. Good luck. On 5 December 2010 18:09, Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote: Hi all, This is a question unrelated to gromacs but would pose it anyway to get some hints from the experts. I wish to set up DNA and DPPC lipid membrane simulation. Could someone please refer to a relevant forcefield/tutorial for simulation of lipids with DNA? Any help will be really appreciated. Thank you amit -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu mailto:itamar.k...@monash.edu -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: lateral diffusion coefficients on a spherical surface
Hi, I am forwarding on a message on behalf of one of my colleagues who is having problems sending messages to the list. Please take a look his message and see if you can help him with his problem. Thank you Tom Piggot Original Message Subject:lateral diffusion coefficients on a spherical surface Date: Thu, 2 Dec 2010 08:05:36 + From: Daniel dah1...@soton.ac.uk To: Piggot T. t.pig...@soton.ac.uk Dear Gromacs users, I would like to calculate some lateral diffusion coefficients of molecules on a spherical surface. I realise that there is no gromacs tool that can do this, but I was wondering if there might be a clever way to edit the code for g_msd? I am currently using Gromacs version 4.0.7. Firstly, I would like to calculate the arc length – the approximate displacement across the surface of the sphere, instead of the linear displacement. Secondly, I would like to remove any angular movement resulting from the rotation of the whole sphere. I realise that there may be a way to do this during the simulation using the com_mode set to angular, but is there a way to post process a trajectory to remove the rotation of the whole sphere? Would post processing of the simulation trajectory introduce errors? Thank you very much for your help, Daniel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gmx-users Digest, Vol 79, Issue 167
Err.Est. RMSD Tot-Drift --- Potential -5660485.4765.184 -31.6659 (kJ/mol) Total Energy-4608515.4950.934 -31.7008 (kJ/mol) USE_NO_CHARGE_GROUP_AND_GMX_4.5.3 AND CHARMM parameters settings Energy Average Err.Est. RMSD Tot-Drift --- Potential -568520 24770.264 -165.498 (kJ/mol) Total Energy-463287 24955.755 -165.768 (kJ/mol) I am particularly eager to obtain from you some comments and advices about these findings. Thanks you so much for your help. SA -- Dr Thomas Piggot University of Southampton, UK. -- -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 79, Issue 167 ** -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?
963.702 -2.58102 (kJ/mol) NO_CHARGE_GROUP_PRE_4.5.0 Energy Average Err.Est. RMSD Tot-Drift --- Potential -563933 30777.279 -202.641 (kJ/mol) Total Energy-458346 29960.748 -202.578 (kJ/mol) CHARGE_GROUP_PRE_4.5.0 Energy Average Err.Est. RMSD Tot-Drift --- Potential -561442 8773.826 -49.7596 (kJ/mol) Total Energy-455891 8958.546 -49.7573 (kJ/mol) USE_CHARGE_GROUP_AND_GMX_4.5.3 AND CHARMM parameters settings Energy Average Err.Est. RMSD Tot-Drift --- Potential -5660485.4765.184 -31.6659 (kJ/mol) Total Energy-4608515.4950.934 -31.7008 (kJ/mol) USE_NO_CHARGE_GROUP_AND_GMX_4.5.3 AND CHARMM parameters settings Energy Average Err.Est. RMSD Tot-Drift --- Potential -568520 24770.264 -165.498 (kJ/mol) Total Energy-463287 24955.755 -165.768 (kJ/mol) I am particularly eager to obtain from you some comments and advices about these findings. Thanks you so much for your help. SA -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Charmm36 FF and membrane
As I said please keep all correspondence on the GROMACS mailing list for general GROMACS problems. You can use genconf to increase the size of the membrane. Cheers Tom tusar ban wrote: Thanks for your reply. The link that you have suggested contains the POPE structure. However that is too small (by XY dimension) for my purpose. I am still trying with Charmm36 FF. Regards On Mon, Nov 1, 2010 at 4:21 PM, Thomas Piggot t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk wrote: Hi, This is more of a GROMACS problem than a specific problem related to this lipid conversion so it is best to keep these questions on the GROMACS mailing list (I have copied my reply there). The warning is fairly explanatory, your input POPE structure (for POPE 315) is missing this hydrogen. This means that whatever you did in VMD to generate the structure did not add this hydrogen. You should have been able to solve this by adding the appropriate lines into the .hdb (which is left empty as the user is expected to provide an all-atom lipid input structure, the same as in the CHARMM27 forcefield in GROMACS). I cannot tell why this has not worked without you providing more details of what you did. However, rather than trying to either fix what you did in VMD or add entries into the .hdb, the easiest solution is to your problem is to just use an available CHARMM36 bilayer as input for pdb2gmx: http://terpconnect.umd.edu/~jbklauda/research/download.html http://terpconnect.umd.edu/%7Ejbklauda/research/download.html Cheers Tom tusar ban wrote: Dear Prof.Piggot, I am trying to equilibrate POPE membrane (generated though VMD) using Gromacs 4.5.1 and Charmm36 FF. I have downloaded charmm36.ff.tgz http://www.gromacs.org/@api/deki/files/127/=charmm36.ff.tgz from http://www.gromacs.org/Downloads/User_contributions/Force_fields. When I do pdb2gmx, I get several warnings, all about H-atoms. One such typical warning is WARNING: atom H6Y is missing in residue POPE 315 in the pdb file You might need to add atom H6Y to the hydrogen database of building block POPE in the file lipids.hdb I opened the lipids.hdb file and found that is empty. What could be the reason for this. Is it intentionally kept empty? When I manually prepare the lipids.hdb (following the Gromacs Manual), I could successfully pdb2gmx, energy minimize the POPE membrane. However, I could not equilibrate the minimized structure. During equilibration, mdrun works up to few thousand steps and then started complaining about LJ 1-4 interactions and it crashes. I do not know where I went wrong. Please enlighten me. Best regards. -- Dr. Tusar Bandyopadhyay Theoretical Chemistry Section, Chemistry Group BARC, Trombay Mumbai 400 085 INDIA Tel: 022-2559 0300 email: tusaratb...@gmail.com mailto:tusaratb...@gmail.com mailto:tusaratb...@gmail.com mailto:tusaratb...@gmail.com -- Dr Thomas Piggot University of Southampton, UK. -- Dr. Tusar Bandyopadhyay Theoretical Chemistry Section, Chemistry Group BARC, Trombay Mumbai 400 085 INDIA Tel: 022-2559 0300 email: tusaratb...@gmail.com mailto:tusaratb...@gmail.com -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Charmm36 FF and membrane
Hi, This is more of a GROMACS problem than a specific problem related to this lipid conversion so it is best to keep these questions on the GROMACS mailing list (I have copied my reply there). The warning is fairly explanatory, your input POPE structure (for POPE 315) is missing this hydrogen. This means that whatever you did in VMD to generate the structure did not add this hydrogen. You should have been able to solve this by adding the appropriate lines into the .hdb (which is left empty as the user is expected to provide an all-atom lipid input structure, the same as in the CHARMM27 forcefield in GROMACS). I cannot tell why this has not worked without you providing more details of what you did. However, rather than trying to either fix what you did in VMD or add entries into the .hdb, the easiest solution is to your problem is to just use an available CHARMM36 bilayer as input for pdb2gmx: http://terpconnect.umd.edu/~jbklauda/research/download.html Cheers Tom tusar ban wrote: Dear Prof.Piggot, I am trying to equilibrate POPE membrane (generated though VMD) using Gromacs 4.5.1 and Charmm36 FF. I have downloaded charmm36.ff.tgz http://www.gromacs.org/@api/deki/files/127/=charmm36.ff.tgz from http://www.gromacs.org/Downloads/User_contributions/Force_fields. When I do pdb2gmx, I get several warnings, all about H-atoms. One such typical warning is WARNING: atom H6Y is missing in residue POPE 315 in the pdb file You might need to add atom H6Y to the hydrogen database of building block POPE in the file lipids.hdb I opened the lipids.hdb file and found that is empty. What could be the reason for this. Is it intentionally kept empty? When I manually prepare the lipids.hdb (following the Gromacs Manual), I could successfully pdb2gmx, energy minimize the POPE membrane. However, I could not equilibrate the minimized structure. During equilibration, mdrun works up to few thousand steps and then started complaining about LJ 1-4 interactions and it crashes. I do not know where I went wrong. Please enlighten me. Best regards. -- Dr. Tusar Bandyopadhyay Theoretical Chemistry Section, Chemistry Group BARC, Trombay Mumbai 400 085 INDIA Tel: 022-2559 0300 email: tusaratb...@gmail.com mailto:tusaratb...@gmail.com -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] New release: 4.5.2
Hi, I have a few questions/comments about the application of the single atom charge groups with the CHARMM27 force field that maybe someone can help with: 1. There are some entries in aminoacids.rtp which have not been converted to having every atom in a separate charge group (ASPP, CYS2, GLUP, LSN, HEME, HEO2, O2, C2 and HOH, hopefully I didn't miss any!). I understand these are some of the less commonly used entries, have they been left out for a reason? By the way I also noticed during a quick test for this that there is not an rtp entry for ARGN but it is given as an option by pdb2gmx when using -inter. 2. Relating to 1 are the charge groups in the water models, which have also been left as a water in a single charge group. I think I remember reading somewhere that this is needed for the fast water loops in GROMACS, so I assume this has been done on purpose. My concern is that this is different to the TIP3P and TP3M entries in the aminoacids.rtp file. If this has been done on purpose for the water models, then maybe TIP3 and TP3M should also just have one charge group (as in the HOH entry)? 3. Finally, another concern I have is that when adding termini to a protein (from aminoacids.c.tdb and aminoacids.n.tdb) then the terminal atoms are still added as one charge group by pdb2gmx. I am not sure of a way around this, apart from still using the -nochargegrp option, or having AMBER style rtp entries for the N and C terminal residues (undesirable I am sure). Cheers Tom On 30/10/10 20:56, Rossen Apostolov wrote: Dear Gromacs users and developers, A new bugfix release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz. Here is a list of some of the resolved issues for 4.5.1: * CHARMM force field now has single atom charge groups (pdb2gmx -nochargegrp no longer required) * Made pdb2gmx -chainsep option work * Fixed possible inconvenient npme node choice with pme load between 0.33 and 0.50 which could lead to very slow mdrun performance. * Made Generalized Born gb_algorithm and sa_surface_tension active and added a separate non-polar solvation term to the output. * Fixed issues in Generalized Born code that could cause incorrect results with SSE and all-vs-all inner-loops. * Fixed bug with pressure coupling with nstlist=-1 that resulted in extremely low densities. * Fixed corrupted energy and checkpoint file output with BAR free energy calculations. * Fixed normalization of g_density using only the last frame. * Fixed several issues with cmake * Several minor fixes. Once again big thanks to all developers for their hard work, and to all users for their contributions! Happy simulating! Rossen -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] who has the force field file of gromos45a4
I answered your same question a few days ago on the mailing list. Please search for my answer if you missed it. Cheers Tom Hong, Liang wrote: Dear all, Right now I plan to use the Gromos 45a4 force field to perform a simulation of carbohydrates. However, this force field is absent from the version of Gromacs (both Gomacs v4.0.7 and v 4.5.1) I'm using. If some one has this force field files, could you, please, pass to me? Best, Liang-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromos 45A4
The 45A4 sugar parameters can be found in the 53A6 files. However, I would be very careful using the parameters in these files. If you take a look at the topologies (see the .rtp file) and compare them to the parameters given in the 45A4 paper you will see that most of the topologies in the 53A6 files are not the same as those described in the 45A4 paper (for an obvious example see the dihedrals of trehalose). If I were you I would make my own rtp entries using the information given in the paper. Cheers Tom Hong, Liang wrote: Dear all, I have seen people using Gromos 45A4 force field to simulate sugars in Gromacs. But there is no such force field in the version 4.07 I'm using now. Where can I find the 45A4 force field? Or use some other force filed to replace it? sincerely, Liang-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 lipid bilayers
Hi Sven, Yes I have tested values of rvdw-switch and (unlike in your test) have seen a large impact of the area per lipid. Indeed this can also be seen in the Klauda paper where they show a decreased area per lipid (~63 A^2 to ~58 A^2) in the NAMD DPPC simulations (see the graph in the Supporting Info) using a 1.1 nm cut-off for the switching compared to the 0.8 nm cut-off in their CHARMM simulations. I would suggest sticking to a rvdw-switch of 0.8 nm and using the CHARMM tip3p water. This gives me the closest results in terms of area per lipid for both POPC and DPPC compared to both the Klauda paper (CHARMM results) and experiment. Cheers Tom Sven Jakobtorweihen wrote: Hi there, Tom, thanks for this hint, yes, that is an improvement. I am looking forward to your paper. Berk, I am using switch for vdw. Although for my taste switching from 0.8 to 1.2 was quite large, I used it because the charmm paper used these values. But I just realized that the implementation of the switch is different in gromacs and charmm, I should have seen that earlier. I think I will increase rvdw_switch to 1.0. However, a couple of days ago I tested already the influence of the switching region and it wasn't dramatic, at least for the test case. Nevertheless, matching the settings used in the parametrization is always advisable. Tom, do you have tested any cutoff settings? Cheers, Sven Berk Hess schrieb: Hi, Another comment on your interaction settings. You did not mail if you are using shift or switch for vdw. But I guess that both probably don't match exactly what Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ
Re: [gmx-users] CHARMM36 lipid bilayers
Yes, I was surprised as well. It depends on the value of rvdw-switch. For some systems it can be 10 A^2, for others much smaller. Tom Pär Bjelkmar wrote: I'm a bit surprised that the CHARMM tip3p makes a significant difference, how large is the difference approximately? /Pär Hi Sven, Yes I have tested values of rvdw-switch and (unlike in your test) have seen a large impact of the area per lipid. Indeed this can also be seen in the Klauda paper where they show a decreased area per lipid (~63 A^2 to ~58 A^2) in the NAMD DPPC simulations (see the graph in the Supporting Info) using a 1.1 nm cut-off for the switching compared to the 0.8 nm cut-off in their CHARMM simulations. I would suggest sticking to a rvdw-switch of 0.8 nm and using the CHARMM tip3p water. This gives me the closest results in terms of area per lipid for both POPC and DPPC compared to both the Klauda paper (CHARMM results) and experiment. Cheers Tom Sven Jakobtorweihen wrote: Hi there, Tom, thanks for this hint, yes, that is an improvement. I am looking forward to your paper. Berk, I am using switch for vdw. Although for my taste switching from 0.8 to 1.2 was quite large, I used it because the charmm paper used these values. But I just realized that the implementation of the switch is different in gromacs and charmm, I should have seen that earlier. I think I will increase rvdw_switch to 1.0. However, a couple of days ago I tested already the influence of the switching region and it wasn't dramatic, at least for the test case. Nevertheless, matching the settings used in the parametrization is always advisable. Tom, do you have tested any cutoff settings? Cheers, Sven Berk Hess schrieb: Hi, Another comment on your interaction settings. You did not mail if you are using shift or switch for vdw. But I guess that both probably don't match exactly what Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have a large effect on the area. Berk Date: Thu, 21 Oct 2010 16:47:21 +0100 From: t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 lipid bilayers Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't
Re: [gmx-users] CHARMM36 lipid bilayers
Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduced with gromacs. I run 40 ns NPT simulations with semiisotropic pressure coupling (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and averages were calculated for the last 30 ns. DMPC and POPC at 303 K and DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made with pdb2gmx -nochargegrp. All simulations contained 128 lipids and approximately the same water/lipid ratio (water is TIP3P) as Klauda et al. I started from charmm27 bilayers provided at the Chramm Gui website. I used the following parameters: rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME; rcoulomb=1.00; fourierspacing=0.15; pme_order=6; rcoulomb_switch=0.00; nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt= 0.002 These simulations result in the following area per lipid [A^2/lipid]: DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7 Comparing to the results of Klauda et al (all simulation with the charmm-package, except one): DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1 +/- 0.4 (with NAMD) It is obvious that my simulations with gromacs 4.5.1 give lower areas per lipid for all cases. Considering the deviations observed by Klauda et al. between Charmm and NAMD simulations ( rvdw_switch was only changed slightly in NAMD) could lead to the conclusion that DMPC and POPC are fine. But I am a bit worried about the DPPC result. Did anyone have suggestions how to improve it? Are these differences expected when comparing gromacs and charmm simulations? Did by any chance someone else tested charmm36 bilayers in gromacs? Thanks, Sven -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CHARMM36 Force Field
Hi all, Just to let everyone know that I have uploaded my conversion of the CHARMM36 force field to the GROMACS website. If you are going to use these files then please have a read of the forcefield.doc file for some more information. These lipid parameters have been checked against the conversion by Par Bjelkmar without any differences seen and allow the simulation of membrane protein systems. If anyone has any questions (or thinks they have found any mistakes!) then feel free to contact me (which is probably best done through the mailing list). Cheers Tom Piggot -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] charmm c36 lipids
Hi Par, I have a working version of the CHARMM36 lipids that I converted myself, which I am fairly confident is correct. I shall check your parameters against my ones to confirm everything is the same and report back to the list. I don't see anything which would not work for your script as there are not any major changes to the forcefield in CHARMM36. Cheers Tom Pär Bjelkmar wrote: Hello Sven, Drew and gmx-users, I've gotten requests from users that want to use the c36 CHARMM lipids in GROMACS (see below). So I answer both of you and the rest of the community in this e-mail. I have a script that parses the top and par files of CHARMM force field(s). It's not the most general piece of code there is so it will not be able to convert files that do not follow the format the CHARMM top and par files had when I wrote it (version c32b1). Also, it cannot parse the toppar files (i.e. what's called the toppar stream files in CHARMM). I downloaded the force field from: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_lipid_all36.tgz My script is able to parse the top_lipid_all36.rtf and par_all36_lipid.prm files without any errors and generate the corresponding GROMACS rtp, atp, bonded and nonbonded files. I'm not an CHARMM expert but if they haven't changed the force field considerable lately (by changing parameter definitions and functional forms of the force field for example) the files generated by the script should be the correct GROMACS translation. However, I cannot guarantee that all went well so I would suggest that those of you who are interested in this look through the files and convince yourself that the script did the job before running production runs with these parameters. I've put it on the old (and outdated) port homepage (http://www.dbb.su.se/User:Bjelkmar/Ffcharmm) so that those of you who are interested in this can access and test it. If nothing seems to be wrong after some of you have tested it I'm going to add it to the user contributions on gromacs.org http://gromacs.org. Regards, Pär Bjelkmar 1 okt 2010 kl. 09.53 skrev Sven Jakobtorweihen: Dear Pär Bjelkmar, thanks for implementing the CHARMM force field into GROMACS, that is really useful. Recently the CHARMM developers have introduced an updated lipid force field CHARMM36 for lipids, see Klauda et al. J. Phys. Chem. B, 2010, 114, 7830 (doi: 10.1021/jp101759q). It seems that this is an important improvement over the preceding version. I checked gromacs version 4.5.1 and the git-repository; unfortunately, the charmm36 lipids are not yet available in gromacs. However, I could write some scripts to convert the charmm files to gromacs files, I have the feeling the bonded parameter conversion is straight forward (having the charmm27 files for gromacs), but I fear that transferring the bonded parameters is tedious. So my question is: Do you have by any change already gromacs files for charmm36 lipids? Or are scripts available to convert charmm FF to gromacs FF files? I am aware of the charmm_to_gromacs perl scripts on the gromacs website. But as fare as I know they are not compatible with the official implementation of charmm in gromacs, or am I wrong? Thanks for your help. Best regards, Sven -- * Dr.-Ing. Sven Jakobtorweihen Hamburg University of Technology Institute of Chemical Reaction Engineering / V2 Eissendorfer Str. 38 21073 Hamburg Germany PHONE : ++49 (0) 40 42878 2491 FAX : ++49 (0) 40 42878 2145 E-MAIL: jakobtorwei...@tuhh.de mailto:jakobtorwei...@tuhh.de * 3 sep 2010 kl. 20.56 skrev Drew Bennett: Dear Pr Bjelkmar, I saw on the gromacs mailing list that you have python a script for converting CHARMM ff to GMX. I would greatly appreciate if you could please send it to me. I am trying to use the new CHARMM36 lipids for a simulation with a membrane protein. Thank-you. Drew Bennett -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] cholesterol
I can think of a few cholesterol topologies just off the top of my head: GROMOS43A1-S3 forcefield has an entry for cholesterol There is a stream file for cholesterol available for use with the CHARMM forcefields. There are other available too, you should use google to find them. I have never used any of them so would not like to comment on which to use, this is up to you to decide after a thorough read of the literature. Cheers Tom #ZHAO LINA# wrote: Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] charmm c36 lipids
Hi Par, For a POPC bilayer then both your and my files produce the same tpr's (checked both with gmxcheck and gmxdump). This is pleasing as I not only scripted the conversions but did some parts by hand! I shall check the other lipids to make sure that there are no discrepancies in these. Also for my files I have included the bonded and non-bonded parameters with parameters from CHARMM27 so as to allow simulations in water and with proteins. I want to re-check these before contributing the forcefield to the website, so it will probably be next week before I upload it. Just to let you know I will use your lipids.rtp as it has the atoms in separate charge groups so as to avoid having to use -nochargegrp with pdb2gmx, whilst mine doesn't. I hope this is fine with you. Cheers Tom Pär Bjelkmar wrote: Hi Tom, great do that! If there're no discrepancies and you have tested it we should probably put your version among the user contributions. Let me know how it goes! /Pär Hi Par, I have a working version of the CHARMM36 lipids that I converted myself, which I am fairly confident is correct. I shall check your parameters against my ones to confirm everything is the same and report back to the list. I don't see anything which would not work for your script as there are not any major changes to the forcefield in CHARMM36. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Issue with Atom Types/Charges/Mass when including ATP in gromos53.a6
possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Processing chain 1 'D' (31 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue ATP476 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Now there are 1 residues with 36 atoms Making bonds... Number of bonds was 38, now 38 Generating angles, dihedrals and pairs... Before cleaning: 42 pairs Before cleaning: 80 dihedrals Making cmap torsions...There are 34 dihedrals, 20 impropers, 58 angles 42 pairs, 38 bonds and 0 virtual sites Total mass 196.043 a.m.u. Total charge 0.673 e Writing topology Writing coordinate file... - PLEASE NOTE You have successfully generated a topology from: ATP.pdb. The Gromos53a6 force field and the spc water model are used. - ETON ESAELP -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with pdb2gmx and a new residue
-- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nucleotides for charmm port
Have you looked in the ffnabonded.itp and ffnanonbonded.itp? To me it looks like all of the atom types/bonds/angles are there. I have just made a very quick rtp entry from the stream file (see attached) and it seems to work fine (but please do check it). Note the very large charge groups, so you should use the -nochargegrp option of pdb2gmx. Cheers Tom David Parcej wrote: Hi all, Has anybody managed to use ATP with the charmm27 ff in gromacs 4.5? The forcefield files are missing atom and bond types and angle information. This is available for charmm, but I have only found it in stream file and have no idea how to convert it. It should be possible (for someone smarter than me). cheers Dave -- Dr Thomas Piggot University of Southampton, UK. [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 5 921 3 1 0 [ATP] ; ; from toppar_all27_na_nad_ppi.str. Thomas Piggot 17/9/10 ; [atoms] C4' CN7 0.16 0 H4' HN7 0.09 0 O4' ON6B -0.50 0 C1' CN7B0.16 0 H1' HN7 0.09 0 C5 CN5 0.28 1 N7 NN4-0.71 1 C8 CN4 0.34 1 H8 HN3 0.12 1 N9 NN2-0.05 1 N1 NN3A -0.74 2 C2 CN4 0.50 2 H2 HN3 0.13 2 N3 NN3A -0.75 2 C4 CN5 0.43 2 C6 CN2 0.46 2 N6 NN1-0.77 3 H61 HN1 0.38 3 H62 HN1 0.38 3 C2' CN7B0.14 4 H2'' HN7 0.09 4 O2' ON5-0.66 4 H2' HN5 0.43 4 C3' CN7 0.14 5 H3' HN7 0.09 5 O3' ON5-0.66 5 H3T HN5 0.43 5 C5' CN8B -0.08 6 H5' HN8 0.09 6 H5'' HN8 0.09 6 O5' ON2-0.62 6 PA P 1.50 6 O1A ON3-0.82 6 O2A ON3-0.82 6 O3A ON2-0.74 6 PB P2 1.50 6 O1B ON3-0.82 6 O2B ON3-0.82 6 O3B ON2-0.86 6 PG P2 1.10 6 O1G ON3-0.90 6 O2G ON3-0.90 6 O3G ON3-0.90 6 [bonds] O5' C5' O5' PA PA O1A PA O2A PA O3A O3A PB PB O1B PB O2B PB O3B O3B PG PG O1G PG O2G PG O3G C5' C4' C4' O4' C4' C3' O4' C1' C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 N6 H61 N6 H62 C6 C5 C5 N7 C2' C3' C2' O2' O2' H2' C3' O3' O3' H3T C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' C5' H5'' C8 H8 C2 H2 N1 C6 N3 C2 C4 C5 N7 C8 [impropers] N6 C6 H61 H62 C6 N1 C5 N6 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ARG Charmm gmx 4.5.1
Hi Berk and others, I have been wondering if there was another way to treat the large charge groups for the CHARMM forcefield(s) in GROMACS, rather than using the -nochargegrp option. The reason I ask is because changing every atom to be in individual charge groups changes the forcefield (albeit slightly) from its original implementation and it would be good to be able to use the forcefields in as close a way as possible as to how they were originally used in CHARMM. I suppose another way to do it is to increase the cutoff's, however changing the cutoff's from their original intended values is also undesirable and this can also significantly impact on performance. Whether this is better or worse (in the sense of the difference to how the forcefields were originally used in CHARMM) than using -nochargegrp I am not sure. I also noticed that in version 4.5 there is a rlistlong parameter, could this be used to account for the large charge groups rather than increasing other cutoff's? Can anyone think of any other ways to do this? I have no idea if it be easy/possible to implement an option to use the CHARMM approach for treating charge groups (as I understand it when any atom is within the cutoff then the whole charge group is included). Sorry for the fairly long message and thanks for any insights you can give. Tom Berk Hess wrote: Hi, No, you should never change the charges in a force field! Run pdb2gmx again with the -nochargegrp option. That will make the size of all charge groups a single atom. This will be done automatically in the 4.5.2 release which will be out soon. Berk Date: Fri, 17 Sep 2010 02:32:31 -0700 From: meetnah...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] ARG Charmm gmx 4.5.1 Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13CT2 1ARG CD 40.2 12.011 ; qtot 1.2 14 HA 1ARGHD1 4 0.09 1.008 ; qtot 1.29 15 HA 1ARGHD2 4 0.09 1.008 ; qtot 1.38 16NC2 1ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1ARG CZ 4 0.64 12.011 ; qtot 1.76 19NC2 1ARGNH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1ARG HH12 4 0.46 1.008 ; qtot 1.88 22NC2 1ARGNH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1ARG HH22 4 0.46 1.008 ; qtot 2 to CD0.18 HD10.06 HD20.06 NE-0.7 HE0.4 CZ0.6 NH1-0.8 HH110.5 HH120.5 NH2-0.8 HH210.5 HH220.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] deletion of some water molecules
You can use trjorder to do this Cheers Tom leila karami wrote: Dear gromacs users I did simulation of protein-dna complex in a box with size 7,7,7. There are 5000 water molecule in this box. After full md simulation, I need a pdb or gro file containing only water molecules being exactly environment of pr-dna complex and not water molecules being in edges or rest of box. Is there any way to do that? -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OPLS-AA topologies for ATP
1 0.0 0.12552.0 === On Jun 22, 2010, at 5:07 AM, Efrat Noy wrote: Hi, Does anyone have OPLS-AA topologies for ATP? Thanks, Efrat -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OPLS-AA topologies for ATP
I chose the AMBER ATP for OPLS as I wanted to simulate my system with two different all-atom forcefields and knew that I could use AMBER in GROMACS with these published parameters (through use of the ffamber ports). The only other all-atom forcefield in GROMACS at that time was OPLS and rather than attempt a new parameterisation of ATP for OPLS I first tried these parameters to see how they would perform. For the testing then I am sure if you think about this then you can come up with some idea's of what good tests would be. If not then look for papers where people have done similar things in the past. Again I must reiterate if you wish to simulate ATP with an all-atom forcefield then I would suggest it is currently much easier to use the AMBER forcefields than to use OPLS unless there is a specific reason to use OPLS. Cheers Tom BIN ZHANG wrote: Dear Tom: Thanks for your suggestion. You are absolutely right on doing more testings. I simply haven't figure out what the appropriate test is yet. Could you be more specific about these parameters perform just as well as? What kind of test did you do? Also, is there a reason why you choose Amber over Charmm? Is it more compatible with OPLS? Thanks, Bin On Jun 23, 2010, at 2:48 AM, Thomas Piggot wrote: Well I would suggest you should do some very careful testing to validate the combination of CHARMM charges and one dihedral with the rest of the parameters from OPLS. It is not very common (or generally wise) to mix and match parameters from different forcefields, see: http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization I would also say that you should also take care with the OPLS-AA DNA parameters as these have not been substantially tested/used and so you should double check the atom types for yourself. On the specific topic of ATP for OPLS-AA/L I have performed simulations using the AMBER ATP parameters in OPLS-AA/L (with no changes for anything such as the different combination rules) and have found these parameters perform just as well as with the AMBER forcefields. There will be a section about this (showing the results from some of the tests I performed) in a paper I am currently writing. The AMBER ATP parameters can be found at: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof However, I would also ask is there a specific reason you wish to use OPLS-AA/L? If not then it is probably easier to use one of the AMBER forcefields with these parameters as you do not need to do any testing (or wait for me to publish my work!) Cheers Tom BIN ZHANG wrote: Hi, I recently made up a topology for ADP. You can probably modify it to ATP easily. I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm). The charges are copied from CHARMM27. Also, there is one dihedral angle missing, again, copied from CHARMM. Please let me know if you have any question, suggestion, Cheers, Bin === In the ffoplsaa.rtp file, I added: [ ADP ] [ atoms ] PBopls_440 1.100 0 ;P O1Bopls_441 -0.900 1 ;O O2Bopls_441 -0.900 2 ;O O3Bopls_441 -0.900 3 ;O PAopls_440 1.500 4 ;P O1Aopls_441 -0.820 5 ;O2 O2Aopls_441 -0.820 6 ;O2 O3Aopls_442 -0.740 7 ;OS O5'opls_442 -0.620 8 ;OS C5'opls_443 -0.080 9 ;CT H5''opls_444 0.09010 ;HC H5' opls_444 0.09011 ;HC C4'opls_158 0.16012 ;CT H4'opls_156 0.09013 ;HC O4'opls_180 -0.50014 ;OS C1'opls_158 0.16015 ;CT H1'opls_156 0.09016 ;HC N9opls_354 -0.05017 ;NA C8opls_353 0.34018 ;CK H8opls_359 0.12019 ;H5 N7opls_352 -0.71020 ;NB C5opls_350 0.28021 ;CB C6opls_351 0.46022 ;CA N6opls_356 -0.77023 ;N2 H61opls_357 0.38024 ;H H62opls_358 0.38025 ;H N1opls_346 -0.74026 ;NC C2opls_347 0.50027 ;CQ H2opls_355 0.13028 ;H5 N3opls_348 -0.75029 ;NC C4opls_349 0.43030 ;CB C2'opls_158 0.14031 ;CT H2''opls_156 0.09032 ;HC O2'opls_171 -0.66033 ;OH H2'opls_172 0.43034 ;HO C3'opls_158 0.14035 ;CT H3'opls_156 0.09036 ;HC O3'opls_171 -0.66037 ;OS H3Topls_172 0.43038 [ bonds ] PBO3A PBO1B PBO2B PBO3B O3A PA PAO1A PAO2A PAO5' O3'H3T O5'C5' C5'C4' C4'O4' C4'C3' O4'C1' C1' N9 C1'C2' N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 N6H61 N6H62 C6 C5 C5 N7 C2'C3' C2'O2' O2'H2' C3'O3' C1'H1' C2' H2'' C3'H3' C4'H4' C5'H5' C5' H5'' C8 H8 C2 H2 N1 C6 N3 C2 C4 C5 N7 C8
Re: [gmx-users] CG (MARTINI) parameters for RNA
Hi, The DNA parameters for use with the MARTINI forcefield are not publicly available to download at the moment, however they will be available very soon. I (or someone else from the Khalid group) will let the list know when and where they have been made available. Cheers Tom Itamar Kass wrote: Shalom all, I wish to try and simulate a protein with few RNA bases attached. As I favour speed over accuracy in this case I wish to use the MARTINI model. I could not find RNA/DNA parameters, but noticed that on the site there is a reference to Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP. DNA and lipid bilayers: self-assembly and insertion. J. Royal Soc. Int. 5, S241-S250, 2008. I wonder if someone had those parameters already implemented into the model? It will be nice to get it nicely packed. Or maybe even better, are there any beta parameters to RNA/DNA in a new MARTINI force field? All the best, Itamar -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_bundle issue
Have you tried using the -z option to calculate the angle with respect to to the z axis? I vaguely remember having an issue like this a few years ago and this fixed the problem, sorry I can't be more specific. Cheers Tom Anirban Ghosh wrote: Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 Regards, Anirban -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PMF of ligand transport
Hi, If you defined the reference (r_57) as part of your channel then with pull_geometry=distance you will have problems as the distance between pull_group1 and pull_group0 becomes closer to zero and then the distance becomes positive again. I recently had this with my umbrella sampling simulations. Search for the discussion of things you can do to address this issue on the list. To stop this being a problem in the first place you should have used pull_geometry=position. Cheers Tom Aswathy wrote: Can any one help me please? I looking forward to hear from any of you. Thank you. On Thu, May 6, 2010 at 1:19 PM, Aswathy ammasa...@gmail.com mailto:ammasa...@gmail.com wrote: Ok i will explain you in detail. Initially i pulled the ligand through the protein channel , using the given parameters. pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = r_57 pull_group1 = r_C1 pull_rate1 = 0.01 pull_k1 = 1500 Then I extracted the frames from the trajectory using the perl program provided with tutorial. COM distance I took as nearly 0.12 nm. (But sometimes I failed to obtain frames exactly at that interval, but took nearly at 0.12). Each frame I used for Umbrella sampling for 1ns. Then I checked histograms for overlapping (Some histograms were entirely overlapped and I removed that from the list, where ever gaps i selected new frames and did sampling so that I can get an evenly distributed histograms , I know this will change the overall COM distribution but is there any other way to solve this?) . Finally once I obtained reasonably good overlapped histograms, I plotted PMF using g_wham. The plot was a steeply increasing potential. How can we get increased PMF even when the ligand is reached out of the channel? Did I made any mistake any where , I am confused. Thank you. -Aswathy On Thu, May 6, 2010 at 12:56 PM, Jochen Hub joc...@xray.bmc.uu.se mailto:joc...@xray.bmc.uu.se wrote: Aswathy wrote: Hi gromacs users, I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel. I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling. Histograms are with reasonabvle overlap. Then I used g_wham for plotting PMF considering first 300ps as equilibration. Isn't SMD usually referred to pulling at some finite pulling speed? That would not be umbrella sampling. Anyway, you'll have to provide a lot more data to enable us to help you. Jochen I am getting a plot , but potential is increasing constantly. ie, PMF is not converged as mentioned the tutorial? Do I need to extend the sampling ? or any other reason? Please help me. Thank you. -Aswathy -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Aswathy -- Aswathy -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel
Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option says Input, opt. not Output, opt as I assume it should be. Also when using -min and -max with the -noauto option, the program quits with the error: Fatal error: With -auto, do not give -min or -max This is not a problem as with -min and -max (without specifying -noauto) g_wham switches automatically switches auto off, but I assumed that using -min and -max the -noauto option would have been the 'correct' way to do this. Cheers Tom Jochen Hub wrote: Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella sampling simulations using the following mdp options and I am now attempting to construct the PMF using g_wham. ; Pull code pull= umbrella ; do umbrella sampling pull_geometry = distance ; can't get PMF with direction Hi Tom, if you want to distinguish between above and below, pull_geometry=position would have been your choice. What I would do now is to run g_wham twice with only the histograms from below and a second time only with the histograms from above your reference. YOu'll have to make appropriate tpr-files.dat and pullx-files.dat input files. Note however, that the PMF very close to your reference will be ill-defined since the pull code checked the distance to the reference and not the z-coordinate. Therefore I would remove simulations in which the ion was sometimes above and sometimes below the reference. To ge the full PMF along the z-axis (which is what you probably want) you'll have to do the simulation again (with pull_geometry=position) I'm afraid. I hope this helps, Jochen pull_dim= N N Y; just in the z pull_start = yes ; add com to pull_init1 pull_ngroups= 1; no. of groups to pull pull_group0 = Protein ; reference group pull_group1 = PO4 ; pull group pull_vec1 = 0 0 0; pull_init1 = 0; pull_rate1 = 0.0 ; no change in ref position pull_k1 = 1000 ; force constant for restraint pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps The problem is that when running g_wham (using the following command) g_wham correctly reads all of the tpr and pullx files, however the data for the windows above and below the reference atom (the middle atom of the protein) are both included in the same part of the PMF profile. g_wham_4.0.5 -ix -it -cycl weighted -b 2000 I assume that this is occuring due to the pull_geometry = distance option, as the distance to the reference does not matter if the ion is above or below the reference? So my question is: Is there a way to construct the complete PMF profile with the simulations I have already run? I should also mention that I have tried using the -min and -max options with g_wham (rather than the auto determination of the boundaries) but this just produces outputs that have all the values as nan. I have also tried using g_wham 4.0.7 but with exactly the same issues ,as well as using the pullf.xvg files as input to g_wham. I apologise if I am missing something obvious (or doing something silly!) but any help would be greatly appreciated. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel
Hi again, Just before I reside myself to rerunning a large number of simulations I was wondering if it is possible to just rerun the simulations where the ion is above and below the reference using pull_geometry=position. Then could I combine these with the other simulations where pull_geometry=distance to get the complete PMF? Tom Jochen Hub wrote: Thomas Piggot wrote: Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option says Input, opt. not Output, opt as I assume it should be. Ah thanks. I'll correct that soon. Also when using -min and -max with the -noauto option, the program quits with the error: Fatal error: With -auto, do not give -min or -max Ok, I guess I never checked that case. But as you point out, you don't have to use -noauto when providing min and max, the auto is switched off automatically. Thanks for the feedback, Jochen This is not a problem as with -min and -max (without specifying -noauto) g_wham switches automatically switches auto off, but I assumed that using -min and -max the -noauto option would have been the 'correct' way to do this. Cheers Tom Jochen Hub wrote: Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella sampling simulations using the following mdp options and I am now attempting to construct the PMF using g_wham. ; Pull code pull= umbrella ; do umbrella sampling pull_geometry = distance ; can't get PMF with direction Hi Tom, if you want to distinguish between above and below, pull_geometry=position would have been your choice. What I would do now is to run g_wham twice with only the histograms from below and a second time only with the histograms from above your reference. YOu'll have to make appropriate tpr-files.dat and pullx-files.dat input files. Note however, that the PMF very close to your reference will be ill-defined since the pull code checked the distance to the reference and not the z-coordinate. Therefore I would remove simulations in which the ion was sometimes above and sometimes below the reference. To ge the full PMF along the z-axis (which is what you probably want) you'll have to do the simulation again (with pull_geometry=position) I'm afraid. I hope this helps, Jochen pull_dim= N N Y; just in the z pull_start = yes ; add com to pull_init1 pull_ngroups= 1; no. of groups to pull pull_group0 = Protein ; reference group pull_group1 = PO4 ; pull group pull_vec1 = 0 0 0; pull_init1 = 0; pull_rate1 = 0.0 ; no change in ref position pull_k1 = 1000 ; force constant for restraint pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps The problem is that when running g_wham (using the following command) g_wham correctly reads all of the tpr and pullx files, however the data for the windows above and below the reference atom (the middle atom of the protein) are both included in the same part of the PMF profile. g_wham_4.0.5 -ix -it -cycl weighted -b 2000 I assume that this is occuring due to the pull_geometry = distance option, as the distance to the reference does not matter if the ion is above or below the reference? So my question is: Is there a way to construct the complete PMF profile with the simulations I have already run? I should also mention that I have tried using the -min and -max options with g_wham (rather than the auto determination of the boundaries) but this just produces outputs that have all the values as nan. I have also tried using g_wham 4.0.7 but with exactly the same issues ,as well as using the pullf.xvg files as input to g_wham. I apologise if I am missing something obvious (or doing something silly!) but any help would be greatly appreciated. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel
Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella sampling simulations using the following mdp options and I am now attempting to construct the PMF using g_wham. ; Pull code pull= umbrella ; do umbrella sampling pull_geometry = distance ; can't get PMF with direction pull_dim= N N Y; just in the z pull_start = yes ; add com to pull_init1 pull_ngroups= 1; no. of groups to pull pull_group0 = Protein ; reference group pull_group1 = PO4 ; pull group pull_vec1 = 0 0 0; pull_init1 = 0; pull_rate1 = 0.0 ; no change in ref position pull_k1 = 1000 ; force constant for restraint pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps The problem is that when running g_wham (using the following command) g_wham correctly reads all of the tpr and pullx files, however the data for the windows above and below the reference atom (the middle atom of the protein) are both included in the same part of the PMF profile. g_wham_4.0.5 -ix -it -cycl weighted -b 2000 I assume that this is occuring due to the pull_geometry = distance option, as the distance to the reference does not matter if the ion is above or below the reference? So my question is: Is there a way to construct the complete PMF profile with the simulations I have already run? I should also mention that I have tried using the -min and -max options with g_wham (rather than the auto determination of the boundaries) but this just produces outputs that have all the values as nan. I have also tried using g_wham 4.0.7 but with exactly the same issues ,as well as using the pullf.xvg files as input to g_wham. I apologise if I am missing something obvious (or doing something silly!) but any help would be greatly appreciated. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] parametrization of FAD
FAD has been prameterised previously. IIRC the parameters are in the appendix of the thesis of Anton Feenstra. Try googling for him and you should find it. Cheers Tom Justin A. Lemkul wrote: Giulia Gonnelli wrote: Hello, my name is Giulia Gonnelli and i'm a new user of the software Gromacs. I'm performing an energy minimmization of several proteins containig biological cofactors. I have problems with the cofactor FAD which has not been parametrized yet on the gromos forcefields. I was wondering how to add new parameters fon unrecognised molecules in Gromacs. I found in literature that actually there are some parameters for the FAD cofactor but i don't know how and where do i have to add these parameters. I'm not used to use gromacs so i apologyze for my simple question...and my english too.Thanks. All the necessary components for a reasonable start at an FAD topology are certainly part of the Gromos force fields. The FMN moiety is described in the .rtp file, as well as ATP, which could be used for the other nucleotide. You can piece the topology together from there. I have found that most functional groups are quite transferable between different species in the Gromos parameter sets. So, theoretically, you could write an .rtp entry for FAD and have pdb2gmx build it automatically into your topology. If you have a complete FAD topology that you trust, you can build an .itp file for it. The manual (Chapter 5) is your friend here. Be aware that parameterization in general is a very advanced concept, so if you are going to be dealing with any other cofactors besides FAD, your life will get complicated. Deriving new parameters is a task only suited for experienced users who plan to devote a substantial amount of time (read: weeks or months) to just deriving suitable parameters. The piecemeal approach I describe for FAD seems to work pretty well, but may not always be possible or feasible. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Regards, Giulia Gonnelli -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] parametrization of FAD
I should also say that there are parameters for FADH(-) available for use with the amber forcefields: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof Tom Thomas Piggot wrote: FAD has been prameterised previously. IIRC the parameters are in the appendix of the thesis of Anton Feenstra. Try googling for him and you should find it. Cheers Tom Justin A. Lemkul wrote: Giulia Gonnelli wrote: Hello, my name is Giulia Gonnelli and i'm a new user of the software Gromacs. I'm performing an energy minimmization of several proteins containig biological cofactors. I have problems with the cofactor FAD which has not been parametrized yet on the gromos forcefields. I was wondering how to add new parameters fon unrecognised molecules in Gromacs. I found in literature that actually there are some parameters for the FAD cofactor but i don't know how and where do i have to add these parameters. I'm not used to use gromacs so i apologyze for my simple question...and my english too.Thanks. All the necessary components for a reasonable start at an FAD topology are certainly part of the Gromos force fields. The FMN moiety is described in the .rtp file, as well as ATP, which could be used for the other nucleotide. You can piece the topology together from there. I have found that most functional groups are quite transferable between different species in the Gromos parameter sets. So, theoretically, you could write an .rtp entry for FAD and have pdb2gmx build it automatically into your topology. If you have a complete FAD topology that you trust, you can build an .itp file for it. The manual (Chapter 5) is your friend here. Be aware that parameterization in general is a very advanced concept, so if you are going to be dealing with any other cofactors besides FAD, your life will get complicated. Deriving new parameters is a task only suited for experienced users who plan to devote a substantial amount of time (read: weeks or months) to just deriving suitable parameters. The piecemeal approach I describe for FAD seems to work pretty well, but may not always be possible or feasible. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Regards, Giulia Gonnelli -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: AMBER force fields for ATP
No intrusion, but I have forwarded this to the GROMACS mailing list as all correspondence is best kept there. It gives you have a much greater chance of getting (better) help. The information needed for the parameters is best obtained from the supporting information given with the Carlson paper. The first thing to do is to add an appropriate entry to the .rtp file. For the O3 atom you need to give a new atom type (for example I have it as amber99_68). You then need to add this new amber atom type to the nb.itp and .atp files. The non-bonded parameters of the new O3 atom type are the same as O2, so to add this new atom type to the nb.itp file is trivial, and the same is true for the .atp file. For the bonded parameters you need to edit the bon.itp file. Firstly you need to add an entry into the [bondtypes] section for the O3 P bond. Then you need to add entries into the [angletypes] for the O3 P O3 and O3 P OS angles. Like the non-bonded parameters these are trivial as they are by analogy to the O2 atom type interactions. For the [angletypes] you also need to change the default P OS P values to those given in the supplementary info of the Carlson paper. This could cause a problem if you have another molecule in your system which uses this angle and you don't want it to use the new angle parameters. I did not and so did not worry about changing this value. If you do use this angle in another molecule (and the default values of some of the P dihedrals which will be changed next) then it would be easier to make an .itp file (where you can just override the defualt values by having the new values in the .itp), or introduce a new atom type for the P atom and use this in all the bonds/angles/dihedrals/non-bonded interactions. Finally you need to add in the new proper dihedrals from the supplementary info into the [dihedraltpyes] section. To turn these parameters given into the correct RB format you need to use the equations in the GROMACS manual (4.63 of the GROMACS 3 manual/4.64 GROMACS 4 manual). As with the [angletypes] you need to alter the default CT OS P OS dihedral to the new value from the paper. Hope this all makes sense and is all correct (I did this quite a while ago!). Cheers Tom Alice Chang wrote: Dear Tom, I hope this is not an intrusion, but I saw your answer on the gmx-users mailing list about finding ATP parameters for use in GROMACS. I am trying to solve the same problem, but without his luck! I've examined the PREP and FRCMOD files, as well as the relevant Carlson paper and ffamber files. I've been comparing the amber .itp, .atp, and .rtp files, but I'm not sure what to use for the radius and epsilon values, or how to parametrize the P-OS-P bond. I was wondering, if you don't mind, could you point me in the right direction? Thanks very much, Alice Chang Liao Research Group Columbia University -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Software inconsistency error: Not enough water
://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Software inconsistency error: Not enough water
--- Though my system has sufficient amount of water (19933) molecules. Can not understand the error. Any information would be useful. Chadan -- Chandan kumar Choudhury NCL, Pune INDIA Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ATP for
Are you sure you added it up correctly? I get a number very close to -4. There is no hydrogen on the gamma phosphate as it was parameterised in this way. If the environment in which your ATP is located suggests that the gamma phosphate should be protonated then you need to use other ATP parameters which include this hydrogen (such as those in the GROMOS forcefield). Cheers Tom Chandan Choudhury wrote: Hi Tom!! Thanks for the information. I went through the paper and added the new O3 atom type. One unusual thing I noticed was that the sum of the partial charges on the atoms of AT P at the last column of http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prep file is -12.7145. How come fractional? and the hydrogens of phosphate are missing. How can it be overcome? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Feb 6, 2010 at 1:13 AM, TJ Piggot t.pig...@bristol.ac.uk mailto:t.pig...@bristol.ac.uk wrote: From the Carlson et al. paper where these ATP parameters were published and through choosing the appropriate amber_X atom types from the .atp (and the corresponding values for these types in the nb and bon .itp files). As I mentioned previously you need to add a new O3 atom type to these files based on the information in the Carlson paper. If you have a look at one of the entries from the ffamberXX.rtp file and work out how this is used by pdb2gmx it should become clear what you need to do to add the ATP to the forcefield. Cheers Tom --On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury iitd...@gmail.com mailto:iitd...@gmail.com wrote: Hi Thomas ! Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon values etc. values. Where to get these values Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot t.pig...@bristol.ac.uk mailto:t.pig...@bristol.ac.uk wrote: Not sure about amb2gmx.pl http://amb2gmx.pl or acpypi but you can do this by hand. Consult the GROMACS manual (Chapter 4) for the equations to convert the parameters into GROMACS format. I would also say that the easiest way would be to create a new entry in the .rtp and then also add the appropriate bonded parameters into the bon.itp file, making sure to include the bonded parameters for the new O3 atom type. Do note that you need to also add this new atom type for the O3 oxygen into the .atp file and the non-bonded parameters for the atom type into the nb.itp file. You can also add entries into the .hdb to allow pdb2gmx to add the appropriate hydrogens to your ATP if so desired. If not, your input pdb for pdb2gmx will need to have these hydrogens already included. Cheers Tom Chandan Choudhury wrote: Hello gmx users, I need to use ATP's parameter for amber port in gromacs. The atp.prep and frcmod.phos for ATP can be found at http://www.pharmacy.manchester.ac.uk/bryce/a http://www.pharmacy.manchester.ac.uk/bryce/amber _mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes_ mber http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in ffamber. The program amb2gmx.pl http://amb2gmx.pl http://amb2gmx.pl needs amber to be installed, which is not present. Same with ACPYPI. Any suggestion will be very helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk mailto:t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users
Re: [gmx-users] H2 topology
I think Justin meant genbox -ci Tom Justin A. Lemkul wrote: 011013021-Jyotsna wrote: Dear Mark, Thank you very much for your suggestions. In the enzyme I am trying to simulate , I need to add 100 H2 molecules (H2+dummy). when I tried adding H2 through genion , i came to know genion supports only monoatomic molecules. My aim is to replace 100 water molecules randomly by H2. How should I go about it? genconf -ci -Justin With warm regards Jyotsna , On Tue, 02 Feb 2010 16:51:19 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: *This message was transferred with a trial version of CommuniGate(r) Pro* On 02/02/10 14:23, 011013021-Jyotsna wrote: Dear David, Thank you very much for your help. As per the literature am following , it is mentioned that the bond distance used is 0.7 Angstrom. Where do I incorporate the bond distance parameter in the topology file? See example in chapter 5 of the manual. The problem am facing is that , I am not very clear as to if the distance is between the two Hydrogen atoms of btween the dummy atom and each of the Hydrogen atoms in either side, in which case the total distance becomes 1.4 A. Surely the text of the original article is more clear than that. In any case, from where did you get the number 0.7439756 in your topology? When i mention the bond distance in the topology file , should it be placed under Bond or constraint? The article surely specifies the nature of the bonded interaction. Work out what that is, and then consider the tables in section 5.7.1. Science in general and computational science in particular is very exacting. For your own sake, please cultivate that habit :-) Mark Thank you, Jyotsna Re: [gmx-users] H2 topology David van der Spoel Mon, 01 Feb 2010 04:02:06 -0800 On 2/1/10 10:57 AM, 011013021-Jyotsna wrote: Dear all, I want to run a simulation for an enzyme. It demands me to incorporate a Molecular hydrogen Topology with a dummy atom in between in the simulation in order to study the path of hydrogen in it.The problem is , the topology file I built induces many errors when i come to the energy minimization step. The version of gromacs I am using is 4.0. The topology file I built is as follows [ moleculetype ] ;name nrexcl H2 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass ; total charge 1 H 1 H2 H1 1 0.475 1.00800 ; 0.00 2 H 1 H2 H2 1 0.475 1.00800 ; 0.00 3 DUM 1 H2 DUM 1 -0.950 0.000 [ virtual_sites2 ] ; Site from funct a 3 1 2 1 0.7439756 When ever I insert the hydrogen+dummy atom topology in the protein's .gro file, an error is generated regarding mismatch of residues or the dummy atom having mass 0 . I would be really grateful if anyone could provide me the hydrogen molecule topology and give some pointers towards it. Please print the error message in your mail. Topology look OK, but you need to add a bond or constraint. Also the constant probably has to be 0.5 since you want the vsite in the center of the two atoms. Thank you, Jyotsna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] J-walking REMD
You can try using the TEE-REX module, the GROMACS 3.3.x version has worked for me in the past on a system too large for standard REMD. Tom David Parcej wrote: Dear All Some time ago there was a discussion concerning the problems of REMD for large systems and the possibility of using the REST implementation of the method. Mark, you mentioned that you had coded an implementation Okur method (JCTC, 2006, 2, 420). How did it work and can you make this available? Any other thoughts on REMD for large systems are also appreciated. cheers David -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] decimal charge instead of integer
If using an amber forcefield and GTP/GDP you can use the parameters on the following website. I have used the ATP/ADP ones and have had no problems with many different systems and ATP/ADP conformations with which I used to test these parameters. http://www.pharmacy.manchester.ac.uk/bryce/amber#cof Tom Justin A. Lemkul wrote: Carla Jamous wrote: Thank you Justin, but I ran a simulation before this one with GTP it worked fine. GDP GTP parameters are identical except for GDP having less atoms. This is why I can't understand why I don't get an integer charge while I did in my previous simulation. OK, but this still doesn't help anyone give you any advice. Please refer to my previous post - which case applies to you: almost integer, or way off? It is also potentially faulty logic to suggest that GDP parameters can be generated from GTP parameters by simply chopping off a phosphate. Under most force field parameter sets, the charges on the beta-phosphate will have to change since the electronic properties of the molecule are now different. -Justin Carla On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Hi, In order to run my simulation, I had to insert GDP parameters in ffamber94 (the force field I'm using). However, I'm having a problem with GDP charge. the charge of every charge group in top file should be an integer. But I'm getting a decimal charge which gives me naturally a decimal total charge of my molecule. I checked number of atoms, it's correct, their charge also. But it seems it's having trouble adding charges giving an integer charge. Does anyone have an idea where is the source of the problem? What is the charge? If it is a small difference between an integer and your charge (i.e., the difference between +1. and +2) then there is no problem. The issue there is the inherent limitation of doing a lot of floating-point operations to sum the total charge. If, however, you have a charge of +1.9256 when you wanted +2, then your parameters are simply wrong. -Justin Thanks Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs
If this is the case then I think you have to take David's advice and you will have to patch openmm to get it to do what you want. Or I suppose decide if you really need to use mdrun-openmm rather than normal mdrun. Tom Hans HEINDL wrote: Thanks Tom, It may easily be that the 6- bond type works in mdrun but not in mdrun-openmm. This would be an explanation for the ridiculous force constants Hans Am Mittwoch, den 06.01.2010, 23:15 + schrieb TJ Piggot: Please keep all correspondence on the GROMACS mailing list, it gives you a much greater chance of someone being able to help you. I have used this bond type before and have had no problems (with force constants much smaller than those which you apply). I would make sure that your box is big enough so that this bond is not being applied across the boundary. Otherwise someone else may have more ideas to help you. Tom Forwarded Message Date: Wednesday, January 06, 2010 22:43:20 +0100 From: Hans HEINDL hhei...@terra.es To: TJ Piggot t.pig...@bristol.ac.uk Cc: Subject: simulationg a distance restraint with a type 6 bond in gromacs Hi, As you remember we discussed simulation of a restraint which is not yet implemented in mdrun-openmm by creating a 'bond'. Type 1 bonds did not work but the type 6 did the job but I could not restrain the distance at the value I projected. The distance between the ends of my peptide should remain 57 angstroms and the best I accomplished was holding the distance fairly well for a ns and then it broke down to a much smaller value. (I tried to define the bond with: 1 614 65.761 40 with the energy term for the bond length obviously too small. But even if I got up to 300 000 000 up to 1 000 000 000 I got no proper result. The best results were recieved with 1 614 5 5.671 5.671 5.671 5.671 but even with such an extreme example the distance tended to shrink kind regards Hans HEINDL University of Westminster UK -- End Forwarded Message -- -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
