Re: [gmx-users] Gromacs's FTP site problems
Hi, Thanks for the query... It's worked fine for Justin Lemkul and me this morning. Mark On Thu, Feb 12, 2015 at 9:29 AM, Silvio a Beccara abecc...@science.unitn.it wrote: Good morning, I've been trying to download a Gromacs tarball for a few days now, without success. It looks like Gromacs' FTP site is not working properly (I get the 550 Failed to change directory error). Could anybody please check? Best regards Silvio a Beccara -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to calculate angles (molecules directions)
Dear users, Is there a way in GROMACS to calculate the angle of each molecule with a specified vector in each step? Thank you in advance. Regards, --Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Semiisotropic pressure coupling
Hello All, I am doing all-atom simulation with charmm 36 ff (obtained from reverse CG using the script provided by Tsjerk) The system consists of popc, 21 AA protein, water and ions. After reverse CG I did short EM and 5 ns NVT simulation. However, when I do NPT simulation, the area per lipid drops from 67 ang2 to 57 within 1 ns ( x and y dimensions decrese and z increases). I am using semiisotropic pressure coupling. I have a question regarding that. I noticed in example .mdps and the tutorial by Justin Lemkul http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/npt.mdp http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/md.mdp tau_p is specified, the ref_p and compresibility is same, does not that mean essentially I am doing isotropic coupling? I am confused what values should be used. Please suggest. Thanks, sxn *md.mdp:* ; RUN CONTROL PARAMETERS dt = 0.002 ;nsTEPS = 1250 ;25ns nsTEPS = 2500 ;50ns integrator = md ld-seed = -1 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 5 nstvout = 5 energygrps = Protein Non-Protein ; Output frequency for energies to log file and energy file nstlog = 100 nstcalcenergy= -1 nstenergy= 100 nstxtcout= 500 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 1 rlist ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 fourierspacing = 0.16 pme_order= 4 optimize-fft= yes ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1.0 rvdw = 1.2 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs lincs-order = 6 ; temperature controls tcoupl = v-rescale tc-grps = Protein Non-Protein tau-t = 1.0 1.0 ref-t = 303303 ; Pressure Controls pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau-p = 1.0 ref-p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GAFF and alkynes
On 2/12/15 9:43 AM, Rebeca García Fandiño wrote: Thanks a lot for the suggestions, Justin. In your CO2 tutorial I have seen the comment One cannot effectively build this molecule in the traditional sense, as there are algorithmic reasons why an angle of 180° is not stable during a simulation. I was wondering what happens if I use angle restraints, for example. Would it lead to an unstable simulation? I suppose that if people use virtual sites to treat with linear molecules instead of applying angle restraints, there should be problems with this approximation...is this correct? A restraint is just a biasing potential towards some desired outcome. It's not necessarily even different in form from a normal harmonic interaction, but I'd be hesitant to try to use some angle definition and a restraint on top of that. The GROMACS code indicates there is a linear angle potential, but it doesn't seem to be documented. This was likely added to circumvent the previous problems with these linear species. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Semiisotropic pressure coupling
On 2/12/15 8:15 PM, shivangi nangia wrote: Hello All, I am doing all-atom simulation with charmm 36 ff (obtained from reverse CG using the script provided by Tsjerk) The system consists of popc, 21 AA protein, water and ions. After reverse CG I did short EM and 5 ns NVT simulation. However, when I do NPT simulation, the area per lipid drops from 67 ang2 to 57 within 1 ns ( x and y dimensions decrese and z increases). I am using semiisotropic pressure coupling. I have a question regarding that. I noticed in example .mdps and the tutorial by Justin Lemkul http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/npt.mdp http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/md.mdp tau_p is specified, the ref_p and compresibility is same, does not that mean essentially I am doing isotropic coupling? No, that does not indicate isotropic pressure coupling. The full pressure tensor is used to calculate pressures in the x-y and z dimensions separately. The values of tau_p and compressibility are simply used for calculating the response time of the barostat. The problem is that your nonbonded settings are incorrect: ; nblist cut-off rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 fourierspacing = 0.16 pme_order= 4 optimize-fft= yes ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1.0 rvdw = 1.2 Note that potential switching leads to errors in the lipid force field. You need a buffered neighbor list with force switching. The exact parameters that you should use are listed on http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM. For lipids, you should absolutely not deviate from these settings. The protein and nucleic acid force fields (and the remainder of CHARMM additive models) should use these settings, though they are more forgiving (i.e. potential switching does not lead to noticeable artifacts). With lipids, the requirements are pretty absolute. People frequently report a drop in APL; every time they do, it's because they're using the wrong settings. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Effect of time step size
On 2/12/15 8:55 AM, Faezeh Pousaneh wrote: I see. thanks. Now can I continue simulations with the increased lincs values? or there is something wrong with my model and I should look for the source of unstability? I would do the latter. If conventional settings don't work for conventional applications, you're likely just fixing a symptom of something. -Justin Best regards *Faezeh Pousaneh* On Thu, Feb 12, 2015 at 1:49 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/15 4:58 AM, Faezeh Pousaneh wrote: Dear Justin, Thank you. Yes, both correspond to same setting except dt. No, expected value is not known. I have just tried to re-simulate with different values of lincs_itr and lincs_order (2 and 8 respectively) and I get similar values for densities. Could that be a good solution? In principle, you shouldn't have to do that in situations like these (note the descriptions of these options in the manual indicate only very specific cases should require increasing them beyond default). More likely, the agreement after these changes indicates that there was something unstable about the previous setup, such that the model is not producing reliable physics when you increase dt too much. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Gromacs's FTP site problems
Good morning, I've been trying to download a Gromacs tarball for a few days now, without success. It looks like Gromacs' FTP site is not working properly (I get the 550 Failed to change directory error). Could anybody please check? Best regards Silvio a Beccara -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GAFF and alkynes
Dear Gromacs users, I am trying to simulate an organic molecule containing an alkyne, using GROMACS and the GAFF force field. When I do grompp I get this note, referring to the atoms involved in the triple bond: NOTE 1 [file ligando_gmx.top, line 289]: The bond in molecule-type solute between atoms 17 C12 and 18 C8 has an estimated oscillational period of 1.7e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. The resulting structure from MD simulations is not correct, since the triple bonds should be linear (C-C=C-H), and I observe an angle among the atoms involved. Maybe GAFF is not well optimized for alkynes, or maybe the NOTE suggested by GROMACS is the responsible for this incorrect structure? Thanks a lot for you help in advance! Rebeca Dr. Rebeca Garcia Santiago de Compostela University Spain -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Effect of time step size
Dear Justin, Thank you. Yes, both correspond to same setting except dt. No, expected value is not known. I have just tried to re-simulate with different values of lincs_itr and lincs_order (2 and 8 respectively) and I get similar values for densities. Could that be a good solution? Best, Best regards *Faezeh Pousaneh* On Wed, Feb 11, 2015 at 10:36 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Justin, Thank you. You are right about we must check validity of typologies attached in Gromacs webpage, but I just took it for test of influence of 'time step' on results when I was faced with similar problem in my own defined molecule. I initially was simulating my Lutidine molecule, so let me please give details of it, (running time 15 ns with same .mdp file as I sent before except this time both with Parrinello-Rahman, 230 molecules in rectangular box): dt=0.002 Energy Average Err.Est. RMSD Tot-Drift --- Temperature 289.953 0.035.63283 0.189132 (K) Pressure3.707212.6389.728 -0.136095 (bar) Density 956.957 0.678.573773.32218 (kg/m^3) dt=0.001 Energy Average Err.Est. RMSD Tot-Drift --- Temperature 289.994 0.0335.70319 0.0487858 (K) Pressure1.826891.2376.7712.81752 (bar) Density 967.363 0.588.214922.86186 (kg/m^3) Yes, I let time for relaxation and I ignore those times before equilibration. I do determine time-dependence of parameters like density and etc, but also I check RMSD of lutidine-lutidine in order to carefully collect the data which are stable. But as you see still there are difference in densities? Isn't is big difference? Many thanks Best regards *Faezeh Pousaneh* On Tue, Feb 10, 2015 at 9:49 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/10/15 3:41 PM, Faezeh Pousaneh wrote: Dear Mark, Thank you so much for the reply. I had sent the .mdp file in my previous email (below). In more details I had equilibriuted 1728 methanol (NPT ensemble at T=290 and P=1atm, using all-bond constraint) for long enough time (10 ns) and I am sure I have reached the equilibrium according to RMSD analysis. RMSD of what? I doubt that analysis of any value here. You should determine the time-dependence of quantities of interest, like diffusion constant, density, etc. 1- You are right about time step with constraint, however I have been running for dt=0.002 as well, and I get density 790 kg/m^3. it means that still there is a big difference in result of dt=0.001 and dt=0.002: 783 kg/m^3 for dt=0.001 790 kg/m^3 for dt=0.002 isn't big difference? then how it is said that dt can be at most 0.002? These are single numbers without error estimates, so there's nothing to be said. If both values are +/- 20, then there's probably no difference. Are you allowing time for relaxation, or are you including all frames (thus some unequilibrated time)? 2- I see that in the experiment the density of ethanol is 791 Kg/m^3 at T=290. That is not in agreement with my result for dt=0.001. What does it mean? does it mean that the given topology of ethanol (I take it from Gromacs homepage) is not well defined? What topology is that? I see methanol for download, but not ethanol. What is the reference for the parameters? If there isn't one, I'd be skeptical about using it. Find a model that has a known (expected) density value, and make sure you can reproduce it using sensible run settings. Note too that from the GROMACS homepage doesn't necessarily imply validity; the user contributions are provided as a convenience but there is no endorsement of correctness; that's for you to evaluate based on publications and your own assessments. integrator= md dt= 0.001 nsteps= 1000 nstxout = 0 ; save coordinates every 0 ps nstvout = 0 ; save velocities every 0 ps nstlog = 0 ; update log file every 2 ps nstenergy = 1000 ; save energies every 2 ps nstxtcout= 10; Output frequency for xtc file xtc-precision = 10; precision for xtc file ; Neighborsearching ns_type = grid; search neighboring grid cells nstlist = 5 ; pbc = xyz ; 3-D PBC rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range
Re: [gmx-users] Semiisotropic pressure coupling
Dear Justin, Thanks for the reply. The link you have mentioned says the parameters are for GROMACS 5.0 I am using an older version, 4.6.1 Is there another link/suggestions for that version. Thanks so much, Best, sxn On 2/12/15 8:15 PM, shivangi nangia wrote: Hello All, I am doing all-atom simulation with charmm 36 ff (obtained from reverse CG using the script provided by Tsjerk) The system consists of popc, 21 AA protein, water and ions. After reverse CG I did short EM and 5 ns NVT simulation. However, when I do NPT simulation, the area per lipid drops from 67 ang2 to 57 within 1 ns ( x and y dimensions decrese and z increases). I am using semiisotropic pressure coupling. I have a question regarding that. I noticed in example .mdps and the tutorial by Justin Lemkul http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/membrane_protein/Files/npt.mdp http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/membrane_protein/Files/md.mdp tau_p is specified, the ref_p and compresibility is same, does not that mean essentially I am doing isotropic coupling? No, that does not indicate isotropic pressure coupling. The full pressure tensor is used to calculate pressures in the x-y and z dimensions separately. The values of tau_p and compressibility are simply used for calculating the response time of the barostat. The problem is that your nonbonded settings are incorrect: ; nblist cut-off rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 fourierspacing = 0.16 pme_order= 4 optimize-fft= yes ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1.0 rvdw = 1.2 Note that potential switching leads to errors in the lipid force field. You need a buffered neighbor list with force switching. The exact parameters that you should use are listed on http://www.gromacs.org/ Documentation/Terminology/Force_Fields/CHARMM. For lipids, you should absolutely not deviate from these settings. The protein and nucleic acid force fields (and the remainder of CHARMM additive models) should use these settings, though they are more forgiving (i.e. potential switching does not lead to noticeable artifacts). With lipids, the requirements are pretty absolute. People frequently report a drop in APL; every time they do, it's because they're using the wrong settings. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] make_ndx selection of backbone residues
Make a group of the or selections first, then run an and on group 4 and your new group. I don't exactly remember, but maybe you can do it in one step by simply putting the 4 at the end instead of the beginning. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of 라지브간디 ra...@kaist.ac.kr Sent: 13 February 2015 00:15 To: gmx-us...@gromacs.org Subject: [gmx-users] make_ndx selection of backbone residues Hi gmx, I would like to know how do I choose the particular residues backbone? Here I intent to select the only specific residues backbone as following way but i guess i am end up with selecting the protein all atoms in residues. 4 r 8-226 | r 242-308 | r 320-410 | r 414-502 | r 521-862 | r 873-1058 | r 1069-1345 (I used this) 0 System : 226391 atoms 1 Protein : 14249 atoms 2 Protein-H : 11094 atoms 3 C-alpha : 1347 atoms 4 Backbone: 4041 atoms 5 MainChain : 5390 atoms 6 MainChain+Cb: 6677 atoms 7 MainChain+H : 6686 atoms 8 SideChain : 7563 atoms 9 SideChain-H : 5704 atoms 10 Prot-Masses : 14249 atoms 11 non-Protein : 212142 atoms 12 Other :36 atoms 13 LIG :36 atoms 14 Water : 212106 atoms 15 SOL : 212106 atoms 16 non-Water : 14285 atoms 17 Backbone__r_8-226_r_242-308_r_320-410_r_414-502_r_521-862_r_873-1058_r_1069-1345: 12493 atoms I suppose to get the backbone selection residues less than backbone (4041 atoms) but it comes 12493 which is close to protein all atoms as i believe i selected the protein all atoms? If so, how do I only select those residues backbone atoms? Appreciated for your info. Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Semiisotropic pressure coupling
Dear Justin: If you have time, can you please provide a link / reference for your comment that potential switching leads to errors in the charmm lipid force field? I tried a google search, but couldn't come up with anything specific. You mentioned noticeable artifacts, so I'm hoping that you can point me at these (or is it just that changing anything about the LJ cutoffs changes the APL, which is pretty general across all lipid force fields in my experience). Thank you, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: 12 February 2015 20:41 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Semiisotropic pressure coupling On 2/12/15 8:15 PM, shivangi nangia wrote: Hello All, I am doing all-atom simulation with charmm 36 ff (obtained from reverse CG using the script provided by Tsjerk) The system consists of popc, 21 AA protein, water and ions. After reverse CG I did short EM and 5 ns NVT simulation. However, when I do NPT simulation, the area per lipid drops from 67 ang2 to 57 within 1 ns ( x and y dimensions decrese and z increases). I am using semiisotropic pressure coupling. I have a question regarding that. I noticed in example .mdps and the tutorial by Justin Lemkul http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/npt.mdp http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/md.mdp tau_p is specified, the ref_p and compresibility is same, does not that mean essentially I am doing isotropic coupling? No, that does not indicate isotropic pressure coupling. The full pressure tensor is used to calculate pressures in the x-y and z dimensions separately. The values of tau_p and compressibility are simply used for calculating the response time of the barostat. The problem is that your nonbonded settings are incorrect: ; nblist cut-off rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 fourierspacing = 0.16 pme_order= 4 optimize-fft= yes ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1.0 rvdw = 1.2 Note that potential switching leads to errors in the lipid force field. You need a buffered neighbor list with force switching. The exact parameters that you should use are listed on http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM. For lipids, you should absolutely not deviate from these settings. The protein and nucleic acid force fields (and the remainder of CHARMM additive models) should use these settings, though they are more forgiving (i.e. potential switching does not lead to noticeable artifacts). With lipids, the requirements are pretty absolute. People frequently report a drop in APL; every time they do, it's because they're using the wrong settings. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster middle
Dear Users: I have run g_cluster from gromacs 4.6.5 as follows: g_cluster -s my.tpr -f tmp.xtc -method gromos -nofit -o rmsd-clust_nofit.xpm -g cluster_nofit.log -sz clust-size_nofit.xvg -cl clusters_nofit.pdb -n index.ndx -cutoff 0.275 -wcl 10 -cl finally.xtc The top of cluster_nofit.log looks like this: Using gromos method for clustering Using RMSD cutoff 0.275 nm The RMSD ranges from 0.0247008 to 5.03412 nm Average RMSD is 0.45568 Number of structures for matrix 12391 Energy of the matrix is 4177.11 nm Found 874 clusters Writing middle structure for each cluster to finally.xtc Writing all structures for the first 10 clusters with more than 1 structures to finally.xtc%03d.xtc cl. | #st rmsd | middle rmsd | cluster members 1 | 4219 0.202 | 784700 .154 | 92900 103300 116100 125900 126500 133000 156600 ... | | | 693900 694000 694200 694300 694600 694700 695700 ... So the frame at 694700 is in the first cluster. However, when I use g_rms to look at the rmsd between frame at 784700 and 694700, I find that the RMSD is 0.29 nm. I am confused because frame 784700 is listed as the middle (which I assume is the cluster centroid) so frame 694700 should not be included in this cluster. When I put these two frames into a single .xtc with only 2 frames, g_cluster correctly puts them into two different clusters when I use a cutoff of 0.275 nm. I understand that some of the members in a cluster can have a pairwise RMSD greater than the cutoff, but I thought that the middle of the cluster should have an RMSD less than the cutoff to all cluster members. Can anybody help me figure out what I am missing? Thank you, Chris. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ffnonbonded.itp and ffbonded.itp files are missing DPPC somehow
Dear gmx-users, I am following the KALP tutorial below:KALP-15 in DPPC Tutorial progress point At this step I get this error (and I know that the discrepancy is because the 23 DPPC molecules are not included): /usr/local/gromacs/bin/gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr Fatal error:number of coordinates in coordinate file (model1_solv.gro, 12266) does not match topology (topol.top, 6) For more information, see my Folder with all of my KALP Tutorial files I see that trying to #include dppc.itp is not the right way to go because it has the same precedence as forcefield.itp. So my guess as to what is wrong is that I messed up the contents of the gromos53a6_lipid.ff folder somehow when I was making them in Step Two of the tutorial. This seems to say that the problem is probably with these two files in the gromos53a6_lipid.ff folder: ffnonbonded.itp and ffbonded.itphttp://comments.gmane.org/gmane.science.biology.gromacs.user/50436 So how do I (manually?) fix the ffnonbonded.itp and ffbonded.itp files? Or did I miss a step in the tutorial? I could redo the tutorial (up to my progress point) pretty quickly. Sincerely,Thomas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] make_ndx selection of backbone residues
Hi gmx, I would like to know how do I choose the particular residues backbone? Here I intent to select the only specific residues backbone as following way but i guess i am end up with selecting the protein all atoms in residues. 4 r 8-226 | r 242-308 | r 320-410 | r 414-502 | r 521-862 | r 873-1058 | r 1069-1345 (I used this) 0 System : 226391 atoms 1 Protein : 14249 atoms 2 Protein-H : 11094 atoms 3 C-alpha : 1347 atoms 4 Backbone: 4041 atoms 5 MainChain : 5390 atoms 6 MainChain+Cb: 6677 atoms 7 MainChain+H : 6686 atoms 8 SideChain : 7563 atoms 9 SideChain-H : 5704 atoms 10 Prot-Masses : 14249 atoms 11 non-Protein : 212142 atoms 12 Other :36 atoms 13 LIG :36 atoms 14 Water : 212106 atoms 15 SOL : 212106 atoms 16 non-Water : 14285 atoms 17 Backbone__r_8-226_r_242-308_r_320-410_r_414-502_r_521-862_r_873-1058_r_1069-1345: 12493 atoms I suppose to get the backbone selection residues less than backbone (4041 atoms) but it comes 12493 which is close to protein all atoms as i believe i selected the protein all atoms? If so, how do I only select those residues backbone atoms? Appreciated for your info. Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: how to calculate angles (molecules directions)
Dear Christopher, I will try the ways you mentioned. One of them should work! I wanted a faster way than writing a code. However, if nothing works, I have to try programming.at last. Thanks a lot! Cheers, --Maryam On Fri, Feb 13, 2015 at 8:51 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Sure.. hope it works. If not, then yes g_traj just gives you the positions, but you know the charges and you can compute the dipole yourself. I know, not an ideal solution, but I was just mentioning it since you may be forced to use it. Even better, write your own gromacs analysis tool by taking a very simple tool and re-purposing it. However, if you don't know C programming, then g_traj + awk can get you most any analyses that you need (though slowly). Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 13 February 2015 00:19 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules directions) Dear Christopher, I tried g_traj -ox but it just gives me the positions not the orientations. I think I should try g_dipole. thank you very much! Cheers, --Maryam On Fri, Feb 13, 2015 at 8:42 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Maryam: I don't know. If g_dipoles doesn't give you what you want (and I have no idea if it will), then g_traj -ox will give you positions that you can then run a script over to compute things yourself. Probably somebody else can offer more advice here. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 12 February 2015 23:59 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules directions) Hi Christopher, You are on the right side! I mean the angle between the dipole moment vector of a molecule and a special vector (for a very simple assumption X axis for example). I found two options g_angle and g_sgangle but I think non of them can help. Are there any other commands to use? thank you! On Fri, Feb 13, 2015 at 8:18 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: How does one compute the angle between a vector and a molecule? I think you need to define your goal more completely. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 12 February 2015 23:45 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Fwd: how to calculate angles (molecules directions) -- Forwarded message -- From: Maryam Kowsar maryam.kow...@gmail.com Date: Fri, Feb 13, 2015 at 12:14 AM Subject: how to calculate angles (molecules directions) To: gromacs.org_gmx-users@maillist.sys.kth.se Dear users, Is there a way in GROMACS to calculate the angle of each molecule with a specified vector in each step? Thank you in advance. Regards, --Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Semiisotropic pressure coupling
Dear Justin, Thanks for the reply. The link you have mentioned says the parameters are for GROMACS 5.0 I am using an older version, 4.6.1 Is there another link/suggestions for that version. Sorry, I forgot to mention. On trying to use those parameters with my version of GROMACS, I get the error: ERROR 1 [file md.mdp, line 78]: Invalid enum 'force-switch' for variable vdw-modifier, using 'Potential-shift-Verlet' Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None' 'Potential-switch' 'Exact-cutoff' The mdp options manual says: *Force-switch*Smoothly switches the forces to zero between *rvdw-switch* and *rvdw*. This shifts the potential shift over the whole range and switches it to zero at the cut-off. Note that this is more expensive to calculate than a plain cut-off and it is not required for energy conservation, since *Potential-shift* conserves energy just as well Can I use Potential-shift instead of my version? Kindly suggesr. Thanks in advance. On Thu, Feb 12, 2015 at 10:30 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Dear Justin, Thanks for the reply. The link you have mentioned says the parameters are for GROMACS 5.0 I am using an older version, 4.6.1 Is there another link/suggestions for that version. Thanks so much, Best, sxn On 2/12/15 8:15 PM, shivangi nangia wrote: Hello All, I am doing all-atom simulation with charmm 36 ff (obtained from reverse CG using the script provided by Tsjerk) The system consists of popc, 21 AA protein, water and ions. After reverse CG I did short EM and 5 ns NVT simulation. However, when I do NPT simulation, the area per lipid drops from 67 ang2 to 57 within 1 ns ( x and y dimensions decrese and z increases). I am using semiisotropic pressure coupling. I have a question regarding that. I noticed in example .mdps and the tutorial by Justin Lemkul http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/membrane_protein/Files/npt.mdp http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/membrane_protein/Files/md.mdp tau_p is specified, the ref_p and compresibility is same, does not that mean essentially I am doing isotropic coupling? No, that does not indicate isotropic pressure coupling. The full pressure tensor is used to calculate pressures in the x-y and z dimensions separately. The values of tau_p and compressibility are simply used for calculating the response time of the barostat. The problem is that your nonbonded settings are incorrect: ; nblist cut-off rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 fourierspacing = 0.16 pme_order= 4 optimize-fft= yes ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1.0 rvdw = 1.2 Note that potential switching leads to errors in the lipid force field. You need a buffered neighbor list with force switching. The exact parameters that you should use are listed on http://www.gromacs.org/ Documentation/Terminology/Force_Fields/CHARMM. For lipids, you should absolutely not deviate from these settings. The protein and nucleic acid force fields (and the remainder of CHARMM additive models) should use these settings, though they are more forgiving (i.e. potential switching does not lead to noticeable artifacts). With lipids, the requirements are pretty absolute. People frequently report a drop in APL; every time they do, it's because they're using the wrong settings. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Variable force constant in umbrella sampling
Dear gromacs users, I have again some question regarding umbrella sampling. Is it ok to use different force constants in the different umbrella runs? So far I only read papers where they keep it constant but for me it could be useful to vary this along the reactioncoordinate. Best, Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: how to calculate angles (molecules directions)
-- Forwarded message -- From: Maryam Kowsar maryam.kow...@gmail.com Date: Fri, Feb 13, 2015 at 12:14 AM Subject: how to calculate angles (molecules directions) To: gromacs.org_gmx-users@maillist.sys.kth.se Dear users, Is there a way in GROMACS to calculate the angle of each molecule with a specified vector in each step? Thank you in advance. Regards, --Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gromacs
Hi gromacs users, I am working on Sotase A complex simulation, I have done 5 ns simulation, I want to extend simulatiom from 5 to 10 ns, is there any person tell me extending command quickly? Thanks in advance for Justin Lemkul Abid Ali Channa, Junior Research Fellow, Lab No. P-133, Computational Chemistry Unit, Dr .Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi-75270. Karachi-Pakistan. UAN # (92-21) 111-222-292 Ext. (309) Cell # +923013553051 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Variable force constant in umbrella sampling
Dear Daniel: It is perfectly fine to use different force constants for different umbrellas. This is commonly done, for example, when you have a very sharp maximum in your PMF and you need to place a few umbrellas at and near this maximum with very strong force constants in order to get good sampling. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Kortzak, Daniel d.kort...@fz-juelich.de Sent: 12 February 2015 22:58 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Variable force constant in umbrella sampling Dear gromacs users, I have again some question regarding umbrella sampling. Is it ok to use different force constants in the different umbrella runs? So far I only read papers where they keep it constant but for me it could be useful to vary this along the reactioncoordinate. Best, Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: how to calculate angles (molecules directions)
Dear Christopher, I tried g_traj -ox but it just gives me the positions not the orientations. I think I should try g_dipole. thank you very much! Cheers, --Maryam On Fri, Feb 13, 2015 at 8:42 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Maryam: I don't know. If g_dipoles doesn't give you what you want (and I have no idea if it will), then g_traj -ox will give you positions that you can then run a script over to compute things yourself. Probably somebody else can offer more advice here. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 12 February 2015 23:59 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules directions) Hi Christopher, You are on the right side! I mean the angle between the dipole moment vector of a molecule and a special vector (for a very simple assumption X axis for example). I found two options g_angle and g_sgangle but I think non of them can help. Are there any other commands to use? thank you! On Fri, Feb 13, 2015 at 8:18 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: How does one compute the angle between a vector and a molecule? I think you need to define your goal more completely. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 12 February 2015 23:45 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Fwd: how to calculate angles (molecules directions) -- Forwarded message -- From: Maryam Kowsar maryam.kow...@gmail.com Date: Fri, Feb 13, 2015 at 12:14 AM Subject: how to calculate angles (molecules directions) To: gromacs.org_gmx-users@maillist.sys.kth.se Dear users, Is there a way in GROMACS to calculate the angle of each molecule with a specified vector in each step? Thank you in advance. Regards, --Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: how to calculate angles (molecules directions)
How does one compute the angle between a vector and a molecule? I think you need to define your goal more completely. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 12 February 2015 23:45 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Fwd: how to calculate angles (molecules directions) -- Forwarded message -- From: Maryam Kowsar maryam.kow...@gmail.com Date: Fri, Feb 13, 2015 at 12:14 AM Subject: how to calculate angles (molecules directions) To: gromacs.org_gmx-users@maillist.sys.kth.se Dear users, Is there a way in GROMACS to calculate the angle of each molecule with a specified vector in each step? Thank you in advance. Regards, --Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: how to calculate angles (molecules directions)
Sure.. hope it works. If not, then yes g_traj just gives you the positions, but you know the charges and you can compute the dipole yourself. I know, not an ideal solution, but I was just mentioning it since you may be forced to use it. Even better, write your own gromacs analysis tool by taking a very simple tool and re-purposing it. However, if you don't know C programming, then g_traj + awk can get you most any analyses that you need (though slowly). Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 13 February 2015 00:19 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules directions) Dear Christopher, I tried g_traj -ox but it just gives me the positions not the orientations. I think I should try g_dipole. thank you very much! Cheers, --Maryam On Fri, Feb 13, 2015 at 8:42 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Maryam: I don't know. If g_dipoles doesn't give you what you want (and I have no idea if it will), then g_traj -ox will give you positions that you can then run a script over to compute things yourself. Probably somebody else can offer more advice here. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 12 February 2015 23:59 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules directions) Hi Christopher, You are on the right side! I mean the angle between the dipole moment vector of a molecule and a special vector (for a very simple assumption X axis for example). I found two options g_angle and g_sgangle but I think non of them can help. Are there any other commands to use? thank you! On Fri, Feb 13, 2015 at 8:18 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: How does one compute the angle between a vector and a molecule? I think you need to define your goal more completely. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 12 February 2015 23:45 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Fwd: how to calculate angles (molecules directions) -- Forwarded message -- From: Maryam Kowsar maryam.kow...@gmail.com Date: Fri, Feb 13, 2015 at 12:14 AM Subject: how to calculate angles (molecules directions) To: gromacs.org_gmx-users@maillist.sys.kth.se Dear users, Is there a way in GROMACS to calculate the angle of each molecule with a specified vector in each step? Thank you in advance. Regards, --Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read
Re: [gmx-users] Fwd: how to calculate angles (molecules directions)
Dear Maryam: I don't know. If g_dipoles doesn't give you what you want (and I have no idea if it will), then g_traj -ox will give you positions that you can then run a script over to compute things yourself. Probably somebody else can offer more advice here. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 12 February 2015 23:59 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules directions) Hi Christopher, You are on the right side! I mean the angle between the dipole moment vector of a molecule and a special vector (for a very simple assumption X axis for example). I found two options g_angle and g_sgangle but I think non of them can help. Are there any other commands to use? thank you! On Fri, Feb 13, 2015 at 8:18 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: How does one compute the angle between a vector and a molecule? I think you need to define your goal more completely. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar maryam.kow...@gmail.com Sent: 12 February 2015 23:45 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Fwd: how to calculate angles (molecules directions) -- Forwarded message -- From: Maryam Kowsar maryam.kow...@gmail.com Date: Fri, Feb 13, 2015 at 12:14 AM Subject: how to calculate angles (molecules directions) To: gromacs.org_gmx-users@maillist.sys.kth.se Dear users, Is there a way in GROMACS to calculate the angle of each molecule with a specified vector in each step? Thank you in advance. Regards, --Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs
(A) modify your .mdp to increase nsteps and then make a new .tpr, then run mdrun -cpi my.cpt files and use the new .tpr file. (B) use tpbconv to modify your original .tpr file and then rerun using mdrun -cpi (C) simply run as before (though you need -cpi option to mdrun since it is a restart) and give mdrun also the option -nsteps (where 250 new steps should give you an additional 5 ns if your timestep is 2 ps). From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Abid Channa abid.cha...@hotmail.com Sent: 12 February 2015 23:56 To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: gmx-us...@gromacs.org Subject: [gmx-users] gromacs Hi gromacs users, I am working on Sotase A complex simulation, I have done 5 ns simulation, I want to extend simulatiom from 5 to 10 ns, is there any person tell me extending command quickly? Thanks in advance for Justin Lemkul Abid Ali Channa, Junior Research Fellow, Lab No. P-133, Computational Chemistry Unit, Dr .Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi-75270. Karachi-Pakistan. UAN # (92-21) 111-222-292 Ext. (309) Cell # +923013553051 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Variable force constant in umbrella sampling
Dear Chris, thanks for this information. What you describe is exactly the situation I ran into. I have a very sharp maximum close to the binding site which is not sampled well with a weak force while in bulk the weak force looks fine. Daniel Dear Daniel: It is perfectly fine to use different force constants for different umbrellas. This is commonly done, for example, when you have a very sharp maximum in your PMF and you need to place a few umbrellas at and near this maximum with very strong force constants in order to get good sampling. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Kortzak, Daniel d.kort...@fz-juelich.de Sent: 12 February 2015 22:58 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Variable force constant in umbrella sampling Dear gromacs users, I have again some question regarding umbrella sampling. Is it ok to use different force constants in the different umbrella runs? So far I only read papers where they keep it constant but for me it could be useful to vary this along the reactioncoordinate. Best, Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs
Add: -cpi state.cpt to your command line. And change your .mpd file to reflect the time you want to use. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Abid Channa [abid.cha...@hotmail.com] Sent: Friday, February 13, 2015 5:56 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: gmx-us...@gromacs.org Subject: [gmx-users] gromacs Hi gromacs users, I am working on Sotase A complex simulation, I have done 5 ns simulation, I want to extend simulatiom from 5 to 10 ns, is there any person tell me extending command quickly? Thanks in advance for Justin Lemkul Abid Ali Channa, Junior Research Fellow, Lab No. P-133, Computational Chemistry Unit, Dr .Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi-75270. Karachi-Pakistan. UAN # (92-21) 111-222-292 Ext. (309) Cell # +923013553051 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs
thanks Christopher Neale for your suggestion , I have done my simulation successfully Abid Ali Channa, Junior Research Fellow, Lab No. P-133, Computational Chemistry Unit, Dr .Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi-75270. Karachi-Pakistan. UAN # (92-21) 111-222-292 Ext. (309) Cell # +923013553051 From: chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org Date: Fri, 13 Feb 2015 05:28:09 + Subject: Re: [gmx-users] gromacs (A) modify your .mdp to increase nsteps and then make a new .tpr, then run mdrun -cpi my.cpt files and use the new .tpr file. (B) use tpbconv to modify your original .tpr file and then rerun using mdrun -cpi (C) simply run as before (though you need -cpi option to mdrun since it is a restart) and give mdrun also the option -nsteps (where 250 new steps should give you an additional 5 ns if your timestep is 2 ps). From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Abid Channa abid.cha...@hotmail.com Sent: 12 February 2015 23:56 To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: gmx-us...@gromacs.org Subject: [gmx-users] gromacs Hi gromacs users, I am working on Sotase A complex simulation, I have done 5 ns simulation, I want to extend simulatiom from 5 to 10 ns, is there any person tell me extending command quickly? Thanks in advance for Justin Lemkul Abid Ali Channa, Junior Research Fellow, Lab No. P-133, Computational Chemistry Unit, Dr .Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi-75270. Karachi-Pakistan. UAN # (92-21) 111-222-292 Ext. (309) Cell # +923013553051 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] What is wrong with enthalpy?
On 2015-02-10 18:58, Igor Shchechkin wrote: Dear Gromacs users, I have changed from 4.5.3 to 4.6.5 version and then continued simulation of Protein+Ligands+water+ions system, having used new created .tpr file and .cpt file produced by the latter run of 4.5.3 version. All went normally, but when I evaluated enthalpy, it appeared to jump from -1.16e6 to -0.67e6. (Earlier I encountered such phenomenon when changed from 4.5.3 to 4.5.5) What is the cause of this? Best regards, Igor Shchechkin How did you extract it? I entered command: g_energy -f Jwi-73.edr -o Jwi-73.VH.xvg then got number-value table, then typed numbers corresponding to Volume (21) and Enthalpy (24). (Volume has jump too, but slight one, unlike enthalpy) Enthalpy = Total Energy + pV I think the main change was to store the Enthalpy directly in the energy file at some point. Please try to check whether the total energy is the same. I chechked total energy; really Enthalpy appears to be equal to Total Energy + pV. In general it is not recommended to change software version during a project. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. spoel at xray.bmc.uu.sehttp://folding.bmc.uu.se Igor Shchechkin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GAFF and alkynes
Thanks a lot for the suggestions, Justin. In your CO2 tutorial I have seen the comment One cannot effectively build this molecule in the traditional sense, as there are algorithmic reasons why an angle of 180° is not stable during a simulation. I was wondering what happens if I use angle restraints, for example. Would it lead to an unstable simulation? I suppose that if people use virtual sites to treat with linear molecules instead of applying angle restraints, there should be problems with this approximation...is this correct? Rebeca Dr. Rebeca Garcia Santiago de Compostela University Spain From: gromacs.org_gmx-users-requ...@maillist.sys.kth.se Subject: gromacs.org_gmx-users Digest, Vol 130, Issue 35 To: gromacs.org_gmx-users@maillist.sys.kth.se Date: Thu, 12 Feb 2015 14:56:03 +0100 Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Gromacs's FTP site problems (Mark Abraham) 2. Re: Insertion of a carbon nanotube in a system (Justin Lemkul) 3. Re: GAFF and alkynes (Justin Lemkul) 4. Re: Effect of time step size (Justin Lemkul) 5. single strand DNA in hairpin conformation (Urszula Uciechowska) 6. Re: single strand DNA in hairpin conformation (Erik Marklund) 7. Re: Effect of time step size (Faezeh Pousaneh) -- Message: 1 Date: Thu, 12 Feb 2015 12:24:37 +0100 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] Gromacs's FTP site problems Message-ID: camnumas9js44njd6ays67gkrfdz0extsh__b-1k1rpwkdte...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Thanks for the query... It's worked fine for Justin Lemkul and me this morning. Mark On Thu, Feb 12, 2015 at 9:29 AM, Silvio a Beccara abecc...@science.unitn.it wrote: Good morning, I've been trying to download a Gromacs tarball for a few days now, without success. It looks like Gromacs' FTP site is not working properly (I get the 550 Failed to change directory error). Could anybody please check? Best regards Silvio a Beccara -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Message: 2 Date: Thu, 12 Feb 2015 07:44:00 -0500 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Insertion of a carbon nanotube in a system Message-ID: 54dca010.8040...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 2/11/15 11:29 PM, soumadwip ghosh wrote: Dear users, I am currently working in the direction of adsorption of nucleic acids on the surface of single-wall carbon nanotubes (SWCNT) and I have made a SWCNT with indices (3,3) using the package Tubegen. What I dont know is how to insert it in my system containing nucleic acids, solvent and ions. Is it possible to add the SWCNT just by making the topology by altering the atom types with the help of pdb2gmx and then add it by using -ci -nmol options of the genbox? Can I use packmole to generate the initial structure by putting all the nucleic acis.PDB, SWCNT.PDB and spce.PDB together? I saw a paper where the ssDNA-SWCNT has been modeled by using xleap package of AMBER which I dont know how to use. Is there any other simpler way for the above purpose? I hope I'm not asking for much. Generate topologies for the nucleic acid and CNT independently; this will give you two topol.top files. Remove the system-level directives to make each of these an .itp file (see the wiki or manual). Create a new .top that #includes the parent force field, each of the nucleic acid and CNT .itp files, etc. Position the DNA and CNT in a suitable box using editconf independently (using rotation and translation options as needed to create the desired orientation), then concatenate the coordinate files. At this point, you'll have a CNT and DNA in a box, with no solvent. From here on, solvating, adding ions, etc. is the same as any simple
Re: [gmx-users] Effect of time step size
I see. thanks. Now can I continue simulations with the increased lincs values? or there is something wrong with my model and I should look for the source of unstability? Best regards *Faezeh Pousaneh* On Thu, Feb 12, 2015 at 1:49 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/15 4:58 AM, Faezeh Pousaneh wrote: Dear Justin, Thank you. Yes, both correspond to same setting except dt. No, expected value is not known. I have just tried to re-simulate with different values of lincs_itr and lincs_order (2 and 8 respectively) and I get similar values for densities. Could that be a good solution? In principle, you shouldn't have to do that in situations like these (note the descriptions of these options in the manual indicate only very specific cases should require increasing them beyond default). More likely, the agreement after these changes indicates that there was something unstable about the previous setup, such that the model is not producing reliable physics when you increase dt too much. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Effect of time step size
On 2/12/15 4:58 AM, Faezeh Pousaneh wrote: Dear Justin, Thank you. Yes, both correspond to same setting except dt. No, expected value is not known. I have just tried to re-simulate with different values of lincs_itr and lincs_order (2 and 8 respectively) and I get similar values for densities. Could that be a good solution? In principle, you shouldn't have to do that in situations like these (note the descriptions of these options in the manual indicate only very specific cases should require increasing them beyond default). More likely, the agreement after these changes indicates that there was something unstable about the previous setup, such that the model is not producing reliable physics when you increase dt too much. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Insertion of a carbon nanotube in a system
On 2/11/15 11:29 PM, soumadwip ghosh wrote: Dear users, I am currently working in the direction of adsorption of nucleic acids on the surface of single-wall carbon nanotubes (SWCNT) and I have made a SWCNT with indices (3,3) using the package Tubegen. What I dont know is how to insert it in my system containing nucleic acids, solvent and ions. Is it possible to add the SWCNT just by making the topology by altering the atom types with the help of pdb2gmx and then add it by using -ci -nmol options of the genbox? Can I use packmole to generate the initial structure by putting all the nucleic acis.PDB, SWCNT.PDB and spce.PDB together? I saw a paper where the ssDNA-SWCNT has been modeled by using xleap package of AMBER which I dont know how to use. Is there any other simpler way for the above purpose? I hope I'm not asking for much. Generate topologies for the nucleic acid and CNT independently; this will give you two topol.top files. Remove the system-level directives to make each of these an .itp file (see the wiki or manual). Create a new .top that #includes the parent force field, each of the nucleic acid and CNT .itp files, etc. Position the DNA and CNT in a suitable box using editconf independently (using rotation and translation options as needed to create the desired orientation), then concatenate the coordinate files. At this point, you'll have a CNT and DNA in a box, with no solvent. From here on, solvating, adding ions, etc. is the same as any simple system. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GAFF and alkynes
On 2/12/15 4:40 AM, Rebeca García Fandiño wrote: Dear Gromacs users, I am trying to simulate an organic molecule containing an alkyne, using GROMACS and the GAFF force field. When I do grompp I get this note, referring to the atoms involved in the triple bond: NOTE 1 [file ligando_gmx.top, line 289]: The bond in molecule-type solute between atoms 17 C12 and 18 C8 has an estimated oscillational period of 1.7e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. The resulting structure from MD simulations is not correct, since the triple bonds should be linear (C-C=C-H), and I observe an angle among the atoms involved. Maybe GAFF is not well optimized for alkynes, or maybe the NOTE suggested by GROMACS is the responsible for this incorrect structure? The bond vibration issue is separate from angles being represented property. Likely you're not dealing with the linear angle properly (i.e. not defining it correctly in the topology). Another approach is virtual site construction to define a linear moiety, as in my CO2 tutorial or as people have done for, e.g. acetonitrile (see the list archive). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
