[gmx-users] Strong position restrain
shima_arasteh2001 at yahoo.com
Sat Sep 22 11:39:58 CEST 2012
As explained it many times before, I am simulating a system of water, dimer protein and water. I am doing this simulation by getting idea from KALP15-DPPC tutorial.
First of all, when I get the top file, I don't see the section of position restrains in top file. My generated top file is as below:
; Include forcefield parameters
; Include chain topologies
; Include POPC chain topology
; Include water topology
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
; Include topology for ions
[ system ]
Gromacs Runs One Microsecond At Cannonball Speeds
[ molecules ]
; Compound #mols
1. I'd like to know why? Is it not expected?
Secondly, to put a strong position restrain on protein, I added the "Strong position restraints for InflateGRO" after FF section. grompp gives me an error of invalid order:
Syntax error - File strong_posre.itp, line 3
Last line read:
'[ position_restraints ]'
Invalid order for directive position_restraints
2. Would you please give me your suggestion?
Thanks in advance.
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