I was trying to apply restraints on my molecules, however, they were still moving after I put 100000kJ/mol/nm^2 on them. I am sure my topology is correct, so I think maybe its the correlation of atom name that is causing all the troubles. I constructed my pores.itp by entering all the molecule fragments I wanted to keep still, while looking at the in.g96 displayed on vmd. Still, I am not sure where the problem is. Do anyone have any suggestions?
for applying position restraint you should do three-step:
1. generate itp file
make posre.itp file with gmx genrestr command for example:
gmx genrestr -f file.gro -o posre.itp -fc 1000 1000 1000
2.edit topology
you could insert posre.itp file with this pattern
#include "erythritol.itp"
; include position restraint file
# ifdef POSRES
# include posre.itp
#endif
if you want to fix erythritol molecules you should insert posre.itp file after erythritol.itp in topology
3. edit mdp file
you should insert
define= -DPOSRES
in .mdp file to apply position restarint
you could fix more than one molecule in your simulation by this command:
define= -DPOSRES -DPOSRES2 -DPOSRES3
Dear Stephane
Yes, you are right,
I work with GROMACS 5.1.4 and my answer is applicable for this version
My thanks to both of you.
However, as I did all you said above, it kept popping up the error message "Atom index (973) in position_restraints out of bounds (1-18)". Can you give me any hint on what is causing this? My files are as below,
#include "oplsaaff.itp"
#include "eryt.itp"
#ifdef POSRES_ERYT
#include "posre.itp"
#endif
[system]
erythritol_crystal
[molecules]
eryt 432
and posre.itp as below
; position restraints for System of 8439
processes 393845346
procs_running 1
procs_blocked 0
softirq 38533625496 0 2300864643 87342410 1266399015 1789076609 0 1221935382 1674544700 32821657 95870008
[ position_restraints ]
; i funct fcx fcy fcz
1 1 100000 100000 100000
973 1 100000 100000 100000
...
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