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Re: [ESPResSo] pbc wrap

From: Salvador Herrera Velarde
Subject: Re: [ESPResSo] pbc wrap
Date: Wed, 09 Jun 2010 19:25:49 -0500


Thanks (again) Olaf and Tristan for your last responses.
Without using the vmd-plg.tcl file,  I can use "pbc wrap" command in VMD.

However, still I can not get what I need. I need/want to visualize all the molecules in just one vesicle/aggregate but still the molecules are splitting (they are no broken) because of the periodic boundary conditions.

I took a look to two similar problems in vmd mail-list

So, after reading the suggestions what I tried was:
pbc set "35.0 35.0 35.0" -all
set box0 [pbc box_draw -shiftcenterrel "0 0 0" ]
and one of the following commands:
pbc wrap -center com  -all
pbc wrap -center com -compound chain -all
pbc wrap -center com -compound res -all
pbc wrap -center bb -compound res -all
pbc wrap -center bb -compound chain -all

Also I tried using
set sel [atomselect top all]
and then
pbc wrap -centersel $sel -center origin -compound res -all

But without success.  I was wondering if a combination of "join" and "pbc wrap" could work.
I tried but again I failed to wrap all the molecules in one aggregate
Any last suggestion?

Thanks a lot,

P.S. should i move this question to vmd list?

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