[gmx-users] (no subject)

[Mario Fernández Pendás]

Hi,

If you want to preserve the cubic shape of your box you need to choose a
barostat that allows to use the isotropic option. However, when using a
barostat your box size is going to change for sure.

Cheers,
Mario

2015-06-03 10:06 GMT+02:00 Sotirios Dionysios I. Papadatos <
si.papadatos at edu.cut.ac.cy>:

> 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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