i started with the lipid coordinates from peter tieleman and removed the water.
then i added water by genbox.
I did energy minimization followed by position restrain, which I removed
gradually. all of it was done under npt. I carried out npt for 250 ps. During
the next 250 ps npt run the bilayers separated and deformed. > Date: Sat, 15
Dec 2007 09:53:06 -0500> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org>
Subject: RE: [gmx-users] problem with npt> > Quoting pragya chohan <[EMAIL
PROTECTED]>:> > >> >> > I wrote yes to generate velocity. Can that be a reason
for the problem? Since> > I am doing membrane simulation it is advised to do
production runs in npt> > thats the only other difference.> > I think what Mark
was asking for was a bit more detail on how you put your> system together. It
would be helpful to know (step by step) what you did, as> that may highlight a
problem. Also, what do you define as "deformed very> much?" Some fluctuations
are to be expected, and 250 ps is a relatively short> time frame. In some of my
bilayer simulations, the lipids look quite strange> under NVT, but after a
nanosecond or two or NPT they even out and behave> normally.> > -Justin> > >
----------------------------------------> > > Date: Sat, 15 Dec 2007 06:03:27
+1100> > > From: [EMAIL PROTECTED]> > > To: gmx-users@gromacs.org> > > Subject:
Re: [gmx-users] problem with npt> > >> > > pragya chohan wrote:> > > >> > > >
thanks for your help.> > > > My system ran fine for 250 ps but later the
bilayer deformed very much.> > >> > > What was your system preparation protocol
- i.e. minimization and> > > equilibration? See> > >
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation> > >> > > Mark>
> > _______________________________________________> > > gmx-users mailing list
gmx-users@gromacs.org> > > http://www.gromacs.org/mailman/listinfo/gmx-users> >
> Please search the archive at http://www.gromacs.org/search before posting!> >
> Please don't post (un)subscribe requests to the list. Use the> > > www
interface or send it to [EMAIL PROTECTED]> > > Can't post? Read
http://www.gromacs.org/mailing_lists/users.php> >> >
_________________________________________________________________> > Post free
property ads on Yello Classifieds now! www.yello.in> >>
http://ss1.richmedia.in/recurl.asp?pid=220_______________________________________________>
> gmx-users mailing list gmx-users@gromacs.org> >
http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive
at http://www.gromacs.org/search before posting!> > Please don't post
(un)subscribe requests to the list. Use the> > www interface or send it to
[EMAIL PROTECTED]> > Can't post? Read
http://www.gromacs.org/mailing_lists/users.php> >> > > >
========================================> > Justin A. Lemkul> Graduate Research
Assistant> Department of Biochemistry> Virginia Tech> Blacksburg, VA> [EMAIL
PROTECTED] | (540) 231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> >
========================================>
_______________________________________________> gmx-users mailing list
gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at http://www.gromacs.org/search before posting!>
Please don't post (un)subscribe requests to the list. Use the > www interface
or send it to [EMAIL PROTECTED]> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
_________________________________________________________________
Post ads for free - to sell, rent or even buy.www.yello.in
http://ss1.richmedia.in/recurl.asp?pid=186
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
