Dear all!<br><br><br>Recently I've forced with the opposite problem. I have pre-equilbrated bilayer of highter dimensions than I need. How I could reduce lipid number of such bilayer as well as reduce total dimensions of such system ?<br>
<br>E.g I have preequilibrated bilayer consisted of 340 lipids. I want to reduce it to the 200 lipids by the symmetrical deletion of the unnecessary lipids from each side. Is there simplest way to do it ?<br><br>James<br>
<br><div class="gmail_quote">2012/5/28 Jon Kapla <span dir="ltr"><<a href="mailto:jon.kapla@mmk.su.se" target="_blank">jon.kapla@mmk.su.se</a>></span><br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi,<br>
<br>
The easiest solution is probably to write a script that reorders the
structure file (gro for example, just swap the lines in each lipid,
and use "editconf -f file.gro -resnr 1" to renumber) the way it is
written in the topology.<br>
<br>
Cheers<br>
Jon<div><div class="h5"><br>
<br>
On 2012-05-28 08:03, James Starlight wrote:
<blockquote type="cite">Peter,<br>
<br>
Thanks for advise. <br>
<br>
I've found already pre-equilibrated POPC bilayers with 200 lipids.
I've examined that lipids and found that they are very similar to
the berger's lipids (it consists of equal nymber of atoms ) but
the atom order in each lipid is slightly different than in
Tieleman's popc.itp file so during processing of that lipids I've
got error of non-matching atoms. Is there any trivial way to make
new popc.itp based on existing gro file with correct atom order ?<br>
<br>
<br>
James<br>
<br>
<div class="gmail_quote">2012/5/26 Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Either use genbox -cs popc128b.gro or genconf -f popc128b.gro
-nbox x y 0<br>
Tieleman's lipids require you to generate a dummy tpr for use
with trjconv<br>
to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o
popc128b-nopbc.gro<br>
-pbc mol -ur compact) first.<br>
<br>
Lots of people have their own bilayer but they may be for
different FFs<br>
which means the atom naming would not be immediately be
compatible with<br>
your FF; for example mine are built for charmm36 and would
require atom<br>
renaming for another FF, even charmm27.<br>
<div>
<div><br>
On 2012-05-26 11:24:12AM +0400, James Starlight wrote:<br>
> Dear Gromacs Users!<br>
><br>
><br>
> I want to perform MD simulation of my membrane
protein in POPC or POPE<br>
> bilayer using Tieleman's parameters for lipids by
means of gromos united<br>
> atom force field. The main problem is that the
pre-equilibrated bilayers<br>
> wich I found on the Dr. Tieleman's site consist of no
more that 128 lipids<br>
> but I want to simulate my protein with bigger number
of lipids ( for<br>
> example starting from 200 lipids ).<br>
> What should I do in that case ? Could you provide
me with some tools for<br>
> construction of such united-atoms bilayers with
desired dimensions ?<br>
> Finally is there any others pre-equilibrated bilayers
aviable for<br>
> downloading besides Dr. Tieleman's site ?<br>
><br>
><br>
> thanks for your help,<br>
><br>
> James S.<br>
<br>
</div>
</div>
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<span><font color="#888888"><br>
<br>
--<br>
==================================================================<br>
Peter C. Lai | University of
Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>
| Birmingham AL 35294-4461<br>
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_____________________________________________________
Jon Kapla
Division of Physical Chemistry
Dpt. of Materials and Environmental Chemistry (MMK)
Arrhenius Laboratory
Stockholm University
SE-106 91 Stockholm
Pos: PhD Student
Phone: +46 8 16 11 79 (office)
Phone: +46 70 304 19 89 (cell)
E-mail: <a href="mailto:jon.kapla@mmk.su.se" target="_blank">jon.kapla@mmk.su.se</a>
_____________________________________________________
</pre>
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