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

[Tsjerk Wassenaar]

Hi Shankari,

Maybe I'm missing something... (social skills according to some ;)),
but afaik it should function properly. Perhaps having the diagonal
elements 0 poses a problem. Could you in any case post the section on
pressure coupling from your .mdp file as you have it now? Also, you
could try to use pcoupltype = semiisotropic, which requires two
parameters for the compressibility: x/y (0 in your case) and z (1e-5).

Hope it helps,

Tsjerk

On 12/18/06, Sivashangari Gnanasambandam <g0501135 at nus.edu.sg> wrote:
> 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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> > 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
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> >
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623