From: Buddhadev Maiti (chebm_at_langate.gsu.edu)
Date: Tue Apr 12 2011 - 11:06:30 CDT
Dear NAMD Users,
I am facing problem to simulate membrane protein system. The detail information is in below:
System: Two Lipid bilayers + protein + water + ions
Force field: Charmm
Program using for simulation: NAMD-2.7
Simulation protocol: Energy minimization, NVT and NPT with restraining protein, water, ions and headgroups of lipids to compress the box and no undesirable gaps present between the periodic images of box, And also no gaps are in between lipids and protein. Then I gradually scale down the restraint and run for NPT constant area production run basically NPAT production run without any restraint. I am getting unphysical results. The gaps are creating between the periodic images of box basically in corners of the box and also in between protein and lipids. The gaps are growing continuously with production run and waters are entering inside the corners of the box and lipids tailgroups. The system is completely turned out to be problematic.
Could you please give me some suggestions, it will be great help for me.
Have a nice day,
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