[gmx-users] trjconv pbc membrane

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 16 22:28:58 CEST 2008

If you use the new version of Gromacs (3.3.3), there are several options that 
work nicely.  Try each of them separately, probably one of them will work, maybe 
a combination will be necessary based on how much your lipids jump around.

trjconv -center
(choose DPPC for centering)

trjconv -pbc res

trjconv -pbc mol

The last two give somewhat different results, depending on the context, for 
reasons I don't yet understand, but usually one of them works :-)


maite lopez cabezas wrote:
> Hi:
> I equilibrated a DPPC  membrane that I built. I want to take a
> snapshot for doing some protein-membrane simulations, but first i have
> to do somethings for eliminating the lipids out of the box. I have
> tried with pbc and fit options like people say in the list and it
> doesn't work. Anybody can help me, please?
> I did things like that and more too (with many combinations):
> 1)
> trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
> trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
> 2)
> trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc nojump
> trjconv -s a.tpr -f b.xtc -o c.xtc -pbc whole
> trjconv -s a.tpr -f c.xtc -o d.xtc -fit rot+trans
> I'll apreciate any help,
> Maite
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> 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
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list