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 :-)
-Justin
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
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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