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
-------------------------------------------------------
Sincerely,
Shima
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