[gmx-users] can we use Area per lipid: 1.00 nm^2

neha bharti nehabharty123 at gmail.com
Thu Aug 7 14:53:02 CEST 2014

 Hello All

I am trying to perform MD for protein-ligand complex in popc lipid with
Charmm36 force field and also follow Justin A. Lemkul tutorial.
I performed

perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat

followed by energy minimization then,

perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat

followed by energy minimization then after 16 iteration of scaling down by
0.95 I got Area per lipid: 1.00 nm^2.

In 17th iteration  Area per lipid become 0.80 nm^2. but after that when I
visualize the .gro file i.e system_shrink17.gro the ligand molecule is far
from protein and out of lipid.

But till 16th iteration its inside the lipid in its normal position.

Should I perform till 16th iteration which gives area per lipid 1.00 nm^2 ?
Is it a good value for Area per lipid ??

or there is some error in my files.

My topology file is :

; Include forcefield parameters
#include "charmm36_lipid.ff/forcefield.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"

; Include ligand topology
#include "LIG.itp"

; Ligand position restraints
#ifdef POSRES
#include "posre_LIG.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]

; Strong position restraints for InflateGRO
#include "strong_posre.itp"

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

; Include water topology
#include "charmm36_lipid.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_lipid.ff/ions.itp"

[ system ]
; Name
Gyas ROwers Mature At Cryogenic Speed

[ molecules ]
; Compound        #mols
Protein             1
LIG                   1
POPC               128

Please Help

Thank you very much.

With Regards

Neha bharty

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