[gmx-users] about some question on gromacs

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 7 13:14:44 CEST 2008

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.


> 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


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