[gmx-users] problem with equilibration of DLiPC membrane
shemami at ucdavis.edu
Thu Nov 12 19:27:51 CET 2015
Thank you very much for your reply. Yes, I chose the temperature 217K based on this website. But shouldn't I equilibrate DLiPC membrane at application temperature like above 280K?
All the best,
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Catarina A. Carvalheda dos Santos <c.a.c.dossantos at dundee.ac.uk>
Sent: Thursday, November 12, 2015 1:44 AM
To: Discussion list for GROMACS users
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] problem with equilibration of DLiPC membrane
The phase transition temperature of DLiPC is -57 degrees (around 216 K)
according to this
On 11 November 2015 at 18:48, Shiva Emami <shemami at ucdavis.edu> wrote:
> Dear all,
> I'm a new Gromacs user and I'm trying to build a lipid membrane with 450
> DLiPC (18:2) by using 43A1-S3 forcefield.
> For membrane building, first I put a single DLiPC molecule in small box,
> then replicated it in x-y by genconf -nbox to get 450 lipid molecules, then
> got another leaflet by editconf -rotate, followed by catting and combining
> two leaflets, EM, changing Z-dimension of the box, solvation and EM.
> When I equilibrate the membrane at lower temperature like 217 K it goes
> well. But trying equilibration at increased temperatures like 300 K, the
> membrane shrinks too much at NPT equilibration and area per lipid decreases
> to very low values.
> Can anybody help me in this case?
> Many thanks
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Catarina A. Carvalheda
Computational Biology Division
School of Life Sciences
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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