# [gmx-users] Can we run a NPT simulation with fixed lengths inxand y direction?

Sivashangari Gnanasambandam g0501135 at nus.edu.sg
Mon Dec 18 13:21:46 CET 2006

```Hi,

I added three zeros to it. Still I am getting the same error.

shankari

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar
Sent: Monday, December 18, 2006 7:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Can we run a NPT simulation with fixed lengths
inxand y direction?

Hi Sankari,

You missed the off-diagonal elements. Just add three zeroes more for
compressibility.

Cheers,

Tsjerk

On 12/18/06, Sivashangari Gnanasambandam <g0501135 at nus.edu.sg> wrote:
>  Hi, everyone
>  I am running anisotropic pressure coupling as shown below
>
> ;Pressure coupling
> Pcoupl                   = berendsen
> Pcoupltype              =  anisotropic
> tau_p            = 5.0
> compressibility          = 0 0 1e-5
> ref_p            = 1.0
>
> It shows error that it need 6 values. Kindly suggest me how to give
> the input parameter for anisotropic pressure coupling.
>
> Thank you,
> Sankari
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der
> Spoel
> Sent: Monday, December 18, 2006 3:50 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Can we run a NPT simulation with fixed
> lengths inx and y direction?
>
> Hu Zhongqiao wrote:
> > Hi, everyone
> >
> > Can we run a NPT simulation with fixed lengths in x and y direction
> > but with variable length in z?
> >
> > Zhongqiao Hu
> >
> > Lab E5-04-27
> > Tel: 65161946(O)
> > Department of Chemical and Biomolecular Engineering National
> > University of Singapore 117576, Singapore
> >
> >
> >
> >
> > --------------------------------------------------------------------
> > --
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> >
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> yes. use compressibility = 0 0 1e-5
>
>
> --
> David.
> ______________________________________________________________________
> __ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,

> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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