Peter C. Lai wrote:
On 2011-05-25 08:00:32AM -0500, Justin A. Lemkul wrote:
Du Jiangfeng (BIOCH) wrote:
Dear Gromacs Users,
There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms
simulation or coarse grained simulation, but is it possible to get a membrane
with 512 lipids? If so, where?
If you have a 128-lipid membrane:
genconf -f 128.gro -o 512.gro -nbox 2 2 1
Wasn't there a warning about PBC and compact structures when using the PDBs
from Peter Tieleman?
Aren't we supposed to unwrap those structures with trjconv before actually
using them in any sort of meaningful way? See also
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
on generating a dummy tpr for feeding into trjconv.
Sure, you need an intact starting structure before doing anything like this.
There are other sources of membranes, not just Tieleman's site, many of which
have already been corrected for PBC effects. The OP did not state the source of
the 128-lipid membranes in question, so I did not presuppose any particular
starting configuration.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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