[gmx-users] freezegrps changing coordinates in NPT simulations
Hello again, I'm running a simulation with graphene as a periodic molecule. I've frozen the carbons in place in the mdp file using: freezegrps = CG_CE freezedim= Y Y Y but when I run an NPT simulation, the entire system shrinks (including moving the carbons closer together) until it crashes. Everything works fine for NVT and minimization. Are there any tricks to freezing groups in NPT simulations? I've also attached my mdp file. Thank you! Jon -- 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] question about REMD
Hello I am running REMD of 53 replica. First I want to equilibrate them. mpirun -np 106 mdrun_mpi -s topol.tpr -v -multidir REMD[012345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152] I always received the error message: Program mdrun_mpi, VERSION 4.6.5 Source code file: /auto/rcf-proj2/mw1/wangmeng/gromacs-4.6.5/src/gmxlib/main.c, line: 423 Fatal error: The number of nodes (106) is not a multiple of the number of simulations (10) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Any one know how to remove this limitation of 10 runs? Thanks! 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.
Re: [gmx-users] energy minimization problem
Dear Justin, could you please tell me how to get the maximum force of an exact atom? I tried g_traj -of, but did not get any force data. Thanks a lot. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 2:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 3:12 AM, Ming Tang wrote: Dear all, I am working with a triple helix containing around 1000 amino acids per chain using martini force field. After energy minimization until it cannot be minimized any more, I moved to NPT, but got LINCS error after thousands of steps. Following Justin's advice on LINCS error, I checked all of the possible causes in blowing up page, but still did not find the reason. Later, I created a smaller model including 30 amino acids per chain, and found it could be move forward to dynamic simulation smoothly using the same control files. Does this mean that my control files are ok? I noticed that the minimization was not good enough when working with my real triple helix, as it got stuck in a certain atom (Epot does not change). I have tried to change to use cg algorithm, but got no improvement. Could anybody tell me how to further minimize my triple helix. I got stuck here for 3 days. Sounds like your initial geometry is just bad. Inspect the surroundings of the atom with maximum force; that usually gives an indication of what's going on. -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] energy minimization problem
On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full .mdp file of the run that is failing. -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.
[gmx-users] Carbon Nanotube `Y-Junctions'
Dear Gromacs users , Greetings .I am looking for XYZ or PDB file of Carbon nanotube ' Y-junction' . I will be grateful if you can let me know how i can find or make it . Thanks in advance .Best ,Saeed. -- 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.
