anirban polley wrote:
Hi,
I have the following questions.
Are there any other ways to make bilayer other than packmol? I
want to make bilayer (.pdb file).
Yes. Read the genconf documentation; it should give you a reasonable
start. Also, have a thorough look through the list archives, this type
of thing has been discussed before.
I saw that in GROMACS, there is united atom model, then what are
the GROMACS computes in the Deuterium order parameter?
Not all lipid parameters are united-atom, but I'll assume that the ones
you used are :-) Think about basic molecular geometry. Aren't all
those carbon centers sp3 along the lipid chain? Using some basic
geometry, one can infer the hydrogen positions.
When I run the system for long time, the program suddenly crashes and
says segmentation fault without giving any information for the
reasons. Can you say what the probable reasons are for which the
program crashes and says segmentation fault?
Absolutely not. Without better information (screen output), there is no
hope of diagnosing a segfault. We have no idea what you're running, how
you created it, how Gromacs was compiled (and which compilers), etc. If
you want free help, make it easy on us and tell us exactly what's going on.
-Justin
sincerely,
Anirban
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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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