[gmx-users] Lipid membrane partially broken and create huge voids after NVT

sdshine sdshine at gmail.com
Tue Apr 9 11:34:39 CEST 2013

 Gromacs users,

My complex heterogenous system has DPPC+ Protein+ligand. I have packed
lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2 got
after 24th iteration) followed by adding solvent and neutralize the system
by adding CL35 & NA 39, since my system has -3.999 non zero total charge.
Then the minimized system has the energy -2.8989 with Max force= 9.58
converged normally in step 464 step.

I used lipid constraints in the file "DPOSRES_LIPID.itp" before NVT

; position restraint file for DPPC P8
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   8    1       0       0       1000

My topology has the last part...
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"

; Include lig topology
#include "lig.itp"

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

; Include DPPC topology
#include "dppc.itp"

;strong position restraints for DPPC
#include "DPOSRES_LIPID.itp"

; Include water topology
#include "spc.itp"

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

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
complex protein in water

[ molecules ]
; Compound        #mols
Protein_G       1
Lig    		1
DPPC           125
SOL             3199
CL               35
NA               39

There is no grompp error and no problem till NVT, after this equillibration,
half of the DPPC along with SOL is no showing in VMD. Could any suggestions
on this behavior. 

Thanks in advance


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