[gmx-users] protein membrane system

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Dec 25 08:42:30 CET 2012

Hi all,

I'm trying to simulate a system of POPC- Protein- Water- Ion following the Justin's tutorial of Kalp15-DPPC.

I get the system-solved-ion.gro and run energy minimization. I saw some water molecules in em.gro file, therefore, I erase them and then again save the .gro file as a new one.
But when I make a new index file, updated the top file and then go through the NVT simulation, I get this fatal error:

Warning: atom name 33908 in topol.top and em.gro does not match (HW2 - HW1)
Warning: atom name 33909 in topol.top and em.gro does not match (OW - HW2)
Warning: atom name 33910 in topol.top and em.gro does not match (HW1 - OW)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 57]:
  43770 non-matching atom names
  atom names from topol.top will be used
  atom names from em.gro will be ignored

Setting gen_seed to 2957
Velocities were taken from a Maxwell distribution at 310 K

Program grompp, VERSION 4.5.5
Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/readir.c, line: 1406

Fatal error:
38 atoms are not part of any of the T-Coupling groups
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

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