[gmx-users] Ac-CoA topology problem

Hi gmx-users, I am a new user of gromacs. I am trying to simulate a protein with cofactor Acetyl-CoA. I have generated gromacs topology for cofactor using prodrg server. I used OPLS-AA force field. I got the error message " Fatal error: Atomtype OA not found. I couldn't fix this problem. Could an

[gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed

> > Hi > > Recently I successfully installed the gromacs-4.0.5 mpi version. > I could run in 8 cpu. but the speed is very slow. > Total number of atoms in the system is 78424. > while running all 8 cpu showing 95-100% CPU. > > How to speed up the calculation. > > Thanks > >

[gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed

am is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /home/thamu/so

[gmx-users] Re: gmx-users Digest, Vol 62, Issue 57

Hi Mark, Yes I have compared the runtime for single as well as 8 processor . Could you please tell me the right steps to configure GROMACS-MPI version?. Thanks. thamu 2009/6/11 > Send gmx-users mailing list submissions to >gmx-users@gromacs.org > > To subscribe or unsubsc

[gmx-users] Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed

Hi, > i am using openmpi, how to build hostfile and where keep that file > > thamu > > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gro

[gmx-users] Error in hdb file ffG43a1p.hdb

some one help me to solve this error. Thanking you, Yours sincerely, Thamu ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting

[gmx-users] error in ffG43a1p force field

, i got the same error as for phosphotyrosine. I am using gromacs-4.0.2. I would greatly appreciate if some one help me to solve this error. Thanking you, Yours sincerely, Thamu ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Pressure scaling warning

Hi, when I run PR mdrun, i got the following warning message. the program can not run further. Step 481 Warning: Pressure scaling more than 1%. I would greatly appreciate gromacs users suggestions. Thanking you, Yours sincerely, Thamotharan ___ gmx-