[gmx-users] lipids number

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Wed Sep 29 15:08:36 CEST 2010

I have a vague impression about that, seems someone asked similar things before.

I will do a try and see.


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Wednesday, September 29, 2010 9:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] lipids number

#ZHAO LINA# wrote:
> Hi,
> I am not sure someone asked some similar questions before or not.
>  >From Prof. Peter Tieleman's website we can get the 128 lipids pdb file.
> Are there some trick and easy way to multiply those lipids . I mean,
> Suppose I need 640 dppc lipids, how can I get those coordinates easily
> from those dppc128 ones.

You can make integer multiples of a box with genconf -nbox.  Otherwise use
genbox -cs dppc128.pdb -box (x y z) until you get a system of appropriate size.
  There was a very similar post yesterday about this same topic.  I would
suggest you have a look at the information Chris Neale posted about the
specifics of box size (genbox caveats) and the need for proper equilibration.


> Thanks and best regards,
> lina


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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