[gmx-users] Strong position restrain

Shima Arasteh 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 "./charmm36-modified.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_A.itp"
#include "topol_Protein_B.itp"

; Include POPC chain topology
#include "popc.itp"

; Include water topology
#include "./charmm36-modified.ff/tip3p.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include topology for ions
#include "./charmm36-modified.ff/ions.itp"

[ system ]
; Name
Gromacs Runs One Microsecond At Cannonball Speeds

[ molecules ]
; Compound        #mols
Protein_A            1
Protein_B            1

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:
Fatal error:
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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