Re: [gmx-users] about insane.py script on martini website.
Hey :) The system needs to be energy minimized and relaxed after generation. Note that the options -d and -x/-y/-z are exclusive. Only the latter will be used. Cheers, Tsjerk On Mar 11, 2014 6:47 AM, jhosamelly ducut_melsar...@yahoo.com wrote: I want to generate a .gro file for a coarse-grained model of a single DLPC lipid. I learned I can used the insane.py script on martini website. This is the input command I used: python insane.py -d 1 -x 1 -y 1 -z 3 -l DLPC -asym 1 -sol 0 -o dlpc.gro Yes I get an output but I don't think I have the right structure. Thanks. :) -- View this message in context: http://gromacs.5086.x6.nabble.com/about-insane-py-script-on-martini-website-tp5015065.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Problem in extending simulation with state.cpt while changing number of cores
On Tue, Mar 11, 2014 at 6:17 AM, Bappa Ghosh ab54...@gmail.com wrote: Thanks Mark for your reply, I am using gromacs version 4.6.3 with single precision. Also I used state.cpt in mdrun , not in the tpbconv. I apologise for my typing mistake. Please use copy and paste when reporting problems. It's faster for you, and doesn't waste everybody's time. So the command line was as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr mdrun -s 15ns_new.tpr -o last_15ns.trr -cpi state.cpt It's still hard to have confidence that we are trouble shooting the right thing. Have you inspected the log file carefully for reasons and differences why mdrun did not do what you think? Note also that e.g. if there's PME tuning going on (e.g. you switched to/from GPU machine), then the Coul (SR) will not be continuous. The total potential energy should be continuous. (And Coul (SR) is a doubtful metric of anything useful, anyway) Mark On Mon, Mar 10, 2014 at 10:11 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Please always report at least your GROMACS version! tpbconv does not take a -cpi argument, so if that is really your command line, then it is not doing what you think it is doing. Then mdrun has no option but to re-start from the only frame it knows about - the one from which you originally started. Mark On Mon, Mar 10, 2014 at 5:23 PM, Bappa Ghosh ab54...@gmail.com wrote: Hello all, I was simulating a mixture of water and carbon-di-oxide for 20ns in one node with 32 cores. After completion of 20ns run' I extended it for further 15ns with tpbconv as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt mdrun -s 15ns_new.tpr -o last_15ns.trr The last 15ns run was carried out in one node with 12 cores. When I plot coulomb potential energy (short range) for whole 35ns trajectory, I observe a sharp rise at the extention time (i.e at the begining of last 15ns run). This sharp rise is not observed if the number of cores are kept same during extension. Any comments/suggestions on this observation will be beneficial to me. Thanks in advance. Bappa Ghosh Project Student .. C/O -Dr Sudip Roy Scientist, CSIR-National Chemical Laboratory, Pune-411008,India -- 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.
[gmx-users] Simulation with Ligand
Dear users, Is it absolutely essential to position restrain the ligand during equilibration step before going for production run for a protein-ligand simulation? Thank you Regards Kavya -- 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] Using pull code to keep two monomers near each other
PLUMED might be useful in this case : http://www.plumed-code.org You could setup a simulation with http://plumed.github.io/doc-v2.0/user-doc/html/_u_p_p_e_r__w_a_l_l_s.html to achieve your goal. Or, as Justin suggested, it might be more straightforward for you to slightly modify the current Gromacs code. Sebastien Date: Sat, 8 Mar 2014 08:32:37 -0500 From: jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Using pull code to keep two monomers near each other On 3/7/14, 7:19 PM, Michael Daily wrote: Hi, I am trying to use the pull code to keep two peptide monomers near each other during a replica exchange simulation of (homo)dimerization. I do not want any bias if the COM distance between the two is less than some value r_max, as in umbrella sampling, i.e. E = 0 for r_ij = r_max; E = k*(r_ij - r_max) for r_ij r_max Can this be done with the pull code or some other function? Pull=constraint appears to essentially fix the COM distance, which I do not want to do either. There is presently no flat-bottom potential implemented in the pull code, but one is planned for version 5.1. In the meantime, it should be relatively easy to add yourself, though, especially if you use a harmonic potential rather than a linear one beyond r_max, then it's just a very simple extension of the existing harmonic potential. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] parameters problem
Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well as [molecule] entry. I have followed the following procedure to #include while creating my first molecule: Run pdb2gmx command. Added #include ligand.itp after #include charmm27.ff/forcefield.itp but before [ moleculetype ] ; Namenrexcl Protein_chain_A 3 and added at the end: [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 1 SOL 17063 then I have merged protein and ligand coordinates by inserting ATOM lines from ligand.pdb to *.pdb generated after pdb2gmx command. Then. I run editconf, genbox and finally grompp command. After which I got following error: Fatal error: No such moleculetype LIG My both *.itp and *.pdb files contains LIG. How to rectify the error? Thanks in advance. On Tue, Mar 11, 2014 at 1:39 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Probably you will see that your ligand.itp has an [atomtypes] entry as well as a [molecule] entry, and the former cannot follow any instance of the latter. Such an .itp file must be #included to create the first molecule. You have your protein [molecule] above the #include ligand.itp at the moment, which would cause this problem. Mark On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: To test swiss param parameters, I have generated *.pdb and *.itp files from it. In the genbox command, I have used -ci *.pdb -nmol 2. I have included *.itp in the topology as: ; Include Position restraint file ;#ifdef POSRES ;#include posre.itp ;#endif ;Include ligand topology #include ligand.itp ; Include water topology #include charmm27.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 2 SOL 12904 But after I run grompp command, I get following error: Fatal error: Syntax error - File ligand.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Please help me rectify the problem of the order getting violated although same worked for topology generated by PRODRG. Thanks in advance. On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 8:21 AM, Nidhi Katyal wrote: Thanks Justin. I would also like to know the reliability of parameters generated using swiss param. I have no personal experience with it. My rule is to never trust anything from a black-box server without verifying it and assessing any information about penalties, deviations, etc. that it provides. -Justin On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 2:45 AM, Nidhi Katyal wrote: Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Cutoff electrostatics are horribly inaccurate. The fact that you conveniently see what you hope to when using a plain cutoff is likely by chance. The bigger issue is the use of PRODRG parameters. As I have said numerous times on this list, the parameters it produces are demonstrably inaccurate and require reparametrization. http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA
[gmx-users] swm4-ndp water with anisotropic polarizibility
Hi I'm trying to set up a slightly modified version of swm4-ndp water with anisotropic polarizibility. In contrast to sw-water, where the Drude (shell) particle is connected to a dummy particle, it is connected to the oxygen in swm4-ndp. In sw.itp, ananisotropic polarizibility is defined by: [ water_polarization ] ; See notes above. Alphas in nm^3 (See ref. above) ; O H H D S funct al_x al_y al_z rOH rHH rOD 1 2 3 4 5 1 0.001415 0.001528 0.001468 0.09572 0.15139 0.0137408 I guess, the 4 5 means that the Drude particle (5) is connected to the dummy particle (4). I therefore changed it to [ water_polarization ] O H H D S funct al_x al_y al_z rOH rHH rOD 1 2 3 1 5 1 0.0010583 0.0011435 0.0010975 0.09572 0.15139 0.0257788 so that Drude particle (5) is now connected to the oxygen (1). This however generates a warning in grompp: WARNING 1 [file swm4-ndp-mod.top, line 33]: Duplicate atom index (1) in water_polarization My question: Is [ water_polarization ] specific for sw-water with the shell particle necessarily connected to the dummy particle, or, can I ignore the warning, or, is there another syntax to do what I want to do (i couldn't find any real description of the syntax of [ water_polarization ]). Best wishes, and thanks in advance for any help you can offer Peter -- 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] swm4-ndp water with anisotropic polarizibility
On 3/11/14, 7:27 AM, Peter Hamm wrote: Hi I'm trying to set up a slightly modified version of swm4-ndp water with anisotropic polarizibility. In contrast to sw-water, where the Drude (shell) particle is connected to a dummy particle, it is connected to the oxygen in swm4-ndp. In sw.itp, ananisotropic polarizibility is defined by: [ water_polarization ] ; See notes above. Alphas in nm^3 (See ref. above) ; O H H D S funct al_x al_y al_z rOH rHH rOD 1 2 3 4 5 1 0.001415 0.001528 0.001468 0.09572 0.15139 0.0137408 I guess, the 4 5 means that the Drude particle (5) is connected to the dummy particle (4). I therefore changed it to [ water_polarization ] O H H D S funct al_x al_y al_z rOH rHH rOD 1 2 3 1 5 1 0.0010583 0.0011435 0.0010975 0.09572 0.15139 0.0257788 so that Drude particle (5) is now connected to the oxygen (1). This however generates a warning in grompp: WARNING 1 [file swm4-ndp-mod.top, line 33]: Duplicate atom index (1) in water_polarization You've repeated atom number 1, which the code is interpreting as both a Drude and the oxygen atom. My question: Is [ water_polarization ] specific for sw-water with the shell particle necessarily connected to the dummy particle, or, can I ignore the warning, or, is there another syntax to do what I want to do (i couldn't find any real description of the syntax of [ water_polarization ]). Best wishes, and thanks in advance for any help you can offer The topology format and the code itself for water polarization is specific to the setup of the SW model. I have been working on generalizing the shell/Drude code for a while now, and the introduction of general anisotropy is not difficult to do, though my implementation is largely untested and therefore not suitable for the public just yet. The code in gmxlib/bondfree.c (water_pol function) can be easily modified. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] g_energy (energygrps)
Dear all I did 20 ns MD simulation on the system with many atoms (containing chain a, b and c of protein). Unfortunately, I forgot to write energygrps (chain a, b and c) in mdp file. My mdrun last long time. Is there any way to obtain new edr file containing chain a, b and c. Any help will highly appreciated. -- 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] g_energy (energygrps)
On 3/11/14, 8:53 AM, Atila Petrosian wrote: Dear all I did 20 ns MD simulation on the system with many atoms (containing chain a, b and c of protein). Unfortunately, I forgot to write energygrps (chain a, b and c) in mdp file. My mdrun last long time. Is there any way to obtain new edr file containing chain a, b and c. This is what mdrun -rerun is for. Create a new .tpr file with the desired energygrps and recalculate the energies. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] choosing Ensemble for production MD run
On Tue, Mar 11, 2014 at 1:30 PM, Archana Sonawani-Jagtap ask.arch...@gmail.com wrote: Hi Everyone, I would like to know if we can run production MD simulation without pressure coupling for protein-ligand simulation? Yes. Whether that will produce something scientifically relevant is up to you. Is it always necessary to have both temperature and pressure coupling in the final md run. No, as above. I have equilibrated the system with NVT followed by NPT and running the simulations using respective cpt files. Will my simulation still have the same properties 300K and 1 bar in the final run as I had used cpt file for final run however I have mentioned Pressure coupling as off? If you equilibrate in NPT, and then switch to NVT, then your simulation will be roughly representative of NPT. The larger it is, the less these differences matter. How to decide which ensemble to use? That depends what you are modelling and why, and secondarily on whether a satisfactory implementation of the desired ensemble exists (generally true in GROMACS). Mark Please help. Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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] g_energy (energygrps)
Use mdrun -rerun on a trajectory with only the frames you care about, and this time with the groups defined. This is how you should intend to do it, because the combined running time will be shorter! Mark On Tue, Mar 11, 2014 at 1:53 PM, Atila Petrosian atila.petros...@gmail.comwrote: Dear all I did 20 ns MD simulation on the system with many atoms (containing chain a, b and c of protein). Unfortunately, I forgot to write energygrps (chain a, b and c) in mdp file. My mdrun last long time. Is there any way to obtain new edr file containing chain a, b and c. Any help will highly appreciated. -- 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_energy (energygrps)
Dear Justin Thanks for your quick reply. I did before: Thus, I should obtain new tpr file from new mdp file with the desired energygrps: grompp -f new.mdp -c *.gro -p *.top -o new.tpr Then, I should use mdrun -s new.tpr -o new.trr -e new.edr -rerun old.trr Are my manner and commands true? Best wishes -- 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_energy (energygrps)
Excuse me In previous post, sentence in line 3 (I did before:) is wrong. -- 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] swm4-ndp water with anisotropic polarizibility
Thanks, Justin, for the quick response. Yes, I can see what to change in gmxlib/bondfree.c Best wishes Peter On 3/11/14, 7:27 AM, Peter Hamm wrote: Hi I'm trying to set up a slightly modified version of swm4-ndp water with anisotropic polarizibility. In contrast to sw-water, where the Drude (shell) particle is connected to a dummy particle, it is connected to the oxygen in swm4-ndp. In sw.itp, ananisotropic polarizibility is defined by: [ water_polarization ] ; See notes above. Alphas in nm^3 (See ref. above) ; O H H D S funct al_x al_y al_z rOH rHH rOD 1 2 3 4 5 1 0.001415 0.001528 0.001468 0.09572 0.15139 0.0137408 I guess, the 4 5 means that the Drude particle (5) is connected to the dummy particle (4). I therefore changed it to [ water_polarization ] O H H D S funct al_x al_y al_z rOH rHH rOD 1 2 3 1 5 1 0.0010583 0.0011435 0.0010975 0.09572 0.15139 0.0257788 so that Drude particle (5) is now connected to the oxygen (1). This however generates a warning in grompp: WARNING 1 [file swm4-ndp-mod.top, line 33]: Duplicate atom index (1) in water_polarization You've repeated atom number 1, which the code is interpreting as both a Drude and the oxygen atom. My question: Is [ water_polarization ] specific for sw-water with the shell particle necessarily connected to the dummy particle, or, can I ignore the warning, or, is there another syntax to do what I want to do (i couldn't find any real description of the syntax of [ water_polarization ]). Best wishes, and thanks in advance for any help you can offer The topology format and the code itself for water polarization is specific to the setup of the SW model. I have been working on generalizing the shell/Drude code for a while now, and the introduction of general anisotropy is not difficult to do, though my implementation is largely untested and therefore not suitable for the public just yet. The code in gmxlib/bondfree.c (water_pol function) can be easily modified. -Justin -- 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] No default Angle types
No default Angle types -- *Mayank Kumar Dixit * Molecular Dynamics lab Department of Chemistry IIT Bombay Powai, Mumbai. Mob No 9820697156 -- 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] No default Angle types
Dear Sir, I wish to inform you that when I am running the command grompp then I am getting errors *No default Angle types* and No *default Ryckaert-Bell. types*. Please suggest solutions as soon as possible Thanks and warn regards -- *Mayank Kumar Dixit * Molecular Dynamics lab Department of Chemistry IIT Bombay Powai, Mumbai. Mob No 9820697156 -- 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] No default Angle types
On 3/11/14, 1:44 PM, Mayank Dixit wrote: Dear Sir, I wish to inform you that when I am running the command grompp then I am getting errors *No default Angle types* and No *default Ryckaert-Bell. types*. Please suggest solutions as soon as possible You've defined interactions that do not exist in the force field. You need to either add suitable parameters or find a force field that can accommodate whatever the interactions are. If you need more specific advice, you need to provide vastly more detail. Search the mailing list archive; this question has been asked and answered hundreds of times. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] Problem with small number of water molecules
On 3/11/14, 2:03 PM, ehs wrote: Hi gmx users, I have tried many ways to simulate a relatively long ionomer chain (340 atoms) solvated in about 100 water molecules, but I did not succeeded yet. The ionomer length is mainly in x direction. For instance, I used the following commands: editconf_d -f conf.gro -bt dodecahedron -box 2 1 1 -d 0.5 -o box.gro genbox_d -cp box.gro -cs spc216.gro -p topol.top -o sol.gro The number of SOL molecules added is 94. However, it is uniformly distributed in the box and only exists in the central region of the box. I ran the energy minimization using sol.gro, but it does not converge to Fmax100. I checked the output file and it seems that all SOL molecules have been shifted to left corner of the box. I hope somebody could help me. That's how genbox works. It tiles the solvent coordinate file starting at the coordinate origin until the box is full or a maximum number of waters have been added. I don't see how the above commands would limit the number of waters to 94. Have you provided the exact commands? Are you using -maxsol? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] Problem with small number of water molecules
Thanks Justin. I didn't use maxsol for this particular example. How can force water to distribute evenly in the box? I thought energy minimization could do it and but in my case, no success so far. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-small-number-of-water-molecules-tp5015086p5015089.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Problem with small number of water molecules
On 3/11/14, 2:24 PM, ehs wrote: Thanks Justin. I didn't use maxsol for this particular example. How can force water to distribute evenly in the box? I thought energy minimization could do it and but in my case, no success so far. I don't know about evenly, but you can do it randomly with genbox -ci -nmol. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P
Hi, When trying to run normal mdrun_mpi with Gromacs 4.6.3 on Bluegene/P, I met this error: Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. The running stops immediately. This is the script for running it: #@ job_name = simulation #@ step_name = step1 #@ comment = Hello World Job #@ error = $(job_name).$(jobid).err #@ output = $(job_name).$(jobid).out #@ environment = COPY_ALL #@ wall_clock_limit = 24:00:00 #@ notification = error #@ job_type = bluegene #@ class = compute #@ bg_size = 128 #@ queue dir=/home/bin/gromacs runDir=production ddir=/bgpscratch/gromacs/$runDir export MDRUN=/opt/apps/gromacs/4.6/bin/mdrun_mpi mkdir -p $ddir cd $ddir /bgsys/drivers/ppcfloor/bin/mpirun -cwd $ddir -mode VN -np 512 -exe $MDRUN -args -s $dir/run.tpr -cpi $ddir/state.cpt -cpo $ddir/state.cpt -maxh 23.9 -npme 128 -noappend I have no idea what can cause that kind of error, could someone offer a help? Thank you, -- View this message in context: http://gromacs.5086.x6.nabble.com/Thread-affinity-error-when-Running-Gromacs-4-6-3-on-Bluegene-P-tp5015095.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] why not coordinates from cpt file
Hi all I have very simple query. While continuing simulations why we need to use *.gro (-c) with grompp as *.cpt (-t) has all the information (as checked with gmxcheck)? cpt file should suffice all the purposes. I tried using grompp providing -t *.cpt file but without -c *.gro file, it does not work. thanks Jiom -- 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] why not coordinates from cpt file
On 3/11/14, 10:36 PM, gromacs query wrote: Hi all I have very simple query. While continuing simulations why we need to use *.gro (-c) with grompp as *.cpt (-t) has all the information (as checked with gmxcheck)? cpt file should suffice all the purposes. I tried using grompp providing -t *.cpt file but without -c *.gro file, it does not work. The .cpt file has all the necessary information related to coordinates, velocities, etc, but grompp still needs a source of atom and residue names, which it gets from the coordinate file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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] error after 1ns of md run during production
I have done the subscription, hope my email will be accepted. Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive, #12-01, Singapore 117599. Tel: (65) 90355220, email: cs...@nus.edu.sg From: Sucharita Dey Sent: Wednesday, March 12, 2014 11:02 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: error after 1ns of md run during production Hello gmx-users, I am running gromacs in a cluster using mpi code, version is 4.5.5, getting the below mentioned error after 1ns run of the production run, before that I have successfully done 50 ps of equilibration. And I checked it is fine. Is the error because of the version? Please help. Following is taken from the log file giving the error: Reading file /hpctmp/csisd/UTX_M//new/UTX_M-final.tpr, VERSION 4.5.5 (single precision) Will use 16 particle-particle and 8 PME only nodes This is a guess, check the performance at the end of the log file Making 2D domain decomposition 8 x 2 x 1 WARNING: This run will generate roughly 7742 Mb of data starting mdrun 'Protein in water' 2500 steps, 5.0 ps. Step 685356, time 1370.71 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 761119.299726, max 9567121.00 (between atoms 2442 and 2443) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2442 2443 90.00.1090 1042816.2500 0.1090 Wrote pdb files with previous and current coordinates [cheetah-c59:mpi_rank_7][error_sighandler] Caught error: Segmentation fault (signal 11) [cheetah-c59:mpi_rank_6][error_sighandler] Caught error: Segmentation fault (signal 11) --- Program mdrun_mpi, VERSION 4.5.5 Source code file: pme.c, line: 538 Fatal error: 3 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Please note, just to check, I ran the same md for 5ns in my PC which has gromacs 4.6.3, and it is running till now uninterrupted (already covered 3ns) Best, -Sucharita -- View this message in context: http://gromacs.5086.x6.nabble.com/error-after-1ns-of-md-run-during-production-tp5015098.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] surprising: what's the reason?
Hi I am testing one MD run using gromacs. 2 days back it ran fine. Today when I ran the exactly same code again, it gave following error: Increasing the number of cell to communicate in dimension X to 3 for the first time --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.3/src/mdlib/ns.c, line: 2730 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. I am confused as to why same run should give different answers on different occasions. Is it pointing to something wrong with the gromacs executable I have or something else? Thank you. regards Chetan -- 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] Regarding calculation of torsion angles in DNA
Hai I am trying to calculate torsional angles in DNA, for that first I made angle.ndx file by using mk_angndx -f prod.tpr -n angle.ndx -type dihedral the out put angle.ndx is looks like as following [ Phi=0.0_3_1.31 ] 12 2 3 412 2 31512 2 316 5 6 7 821 6 7 822 6 7 8 6 7 8 9 6 7 810 6 7 811 23 7 8 923 7 81023 7 811 24 7 8 924 7 81024 7 810 24 7 8113828293038282941 382829423132333447323334 483233343233343532333436 323334374933343549333436 493334375033343550333436 503334365033343764545556 645455676454556857585960 [ Phi=0.0_3_1.34 ] 13 2 3 414 2 3 4 2 3 417 2 3 41815 3 4 516 3 4 5 3 4 519 3 4 52017 4 5 6 18 4 5 6 4 5 621 4 5 622 19 5 6 720 5 6 7 5 6 723 5 6 7243928293040282930 282930432829304441293031 422930312930314529303146 433031324430313230313247 303132484531323346313233 What is the meaning of [ Phi=0.0_3_1.34 ] . I want to find the changes in the torsion angles alpha, beta, gammaa...etc through out the simulation. For this how can i make the index file. Thank You very much. -- regards M.SathishKumar -- 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.
