[gmx-users] Re: size of the molecule

[Ing. Vojtech Spiwok]

> Message: 1
> Date: Thu, 22 Jul 2004 11:15:45 +0100 (BST)
> From: raj vel <rajgrmx at yahoo.co.in>
> Subject: [gmx-users] size of the molecule
> To: gmx-users at gromacs.org
> Message-ID: <20040722101545.93575.qmail at web8306.mail.in.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
> 
> hello all,
> i am unable to do mdrun, for a protein with 504
> aminoacids. while mdrun, LINCS warning and the
> pressure coupling is more than 1 amu and this aborts
> the mdrun. i was informed to increase tau_p, even that
> is not working. 
> but when i split the molecule (from PDB) into 100
> aminoacid each, mdrun runs properly. but the time
> taken by each fragment for mdrun differs very high.(
> 45 min for one segment and 48 hours for another
> segment).
> 
> is that possible to do mdrun for a molecule with such
> high no. of amino acids??
> any suggestions
> thanks in advance.
> 

I use gromacs for 4 x 1000 amino-acids. Please, send
some more details. Do you use solvent?

Vojtech Spiwok
ICT Prague


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