[gmx-users] (no subject)

[Sotirios Dionysios I. Papadatos]

Hi, I'm not accustomed with coarse grained, but from the little stuff I know on MD in order to keep a box's size constant you have to use an NVT simulation not an NPT. Meaning don't keep pressure constant but rather the volume. Do double check though, I might be wrong.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of HongTham <hongtham0709 at gmail.com>
Sent: Friday, May 29, 2015 9:13 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] (no subject)

Dear Gromacs User,
I simulated a coarse grained membrane protein system. This is my pressure
control parameter.
; pressure control
Pcoupl           =  berendsen       ;
Pcoupltype       =  semiisotropic   ;
tau-p            =  5.0 5.0         ;
compressibility  =  4.5e-5 4.5e-5   ;
ref-p            =  1.0 1.0 1.0 1.0 ;
refcoord_scaling = all              ;
Although I set Pcoupltype as semiisotropic, after running simulation a
while, my box was changed from cubic (starting) to rectangular
parallelepiped. the x,y direction were shortened while z direction was
lengthened a lot. is there any option to control the box size through the
simulation?
Thank you so much.
Hongtham
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