[gmx-users] trjconv pbc membrane

[maite lopez cabezas]

Thanks for the quickly answer. I used  3.3.3 and 3.3.1 version and the
lipids of a monocape are above to the other. The lipids are jumping yet
after all those changes. I proved each option separately and some
combinations of them.

trjconv -s a.tpr -f a.xtc -o b.xtc -center
trjconv -s a.tpr -f b.xtc -o c.xtc -pbc whole/res/mol/none
trjconv -s a.tpr -f a.xtc -o b.xtc -center -boxcenter tric
-pbc none (res/whole....) -boxcenter tric -center

and more..

Cheers,
Maite



On 7/16/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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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