>You might try:
>trajin <filename>.crd
>trajout <fileout> restart
>image center
>go
>This worked for me! (using ptraj-6.2 or 6.3)
This may work if the system is not moved too far from the initial structure. It does not work for me as parts of some lipids have moved outside the central box while the rest parts of the lipids remain in the box. How ptraj can handle this?
>I am very interested, because I switched from AMBER to GROMACS (or rather
>I am in the process of switching :-) ). I didn't have the right >tools to
>analyze the properties of my bilayer. How do you do this?
Indeed, I may not have all the right amber forcefield paramters for lipid bilayers. We used some from Charmm and developed a few our own. Someone out there may be trying to make the Charmm forcefiled for lipid bilayers compatible to amber. I would be very interested to know where the source. Amber does not provide enough tools to analyze bilayer properties. We have used ptraj and carnal to calculate some properties but have to write some codes ourselves specifically meet our own need.
T.X. Xiang
"Xiang, Tian-Xiang" wrote:
>
> Dear Sir:
>
> I am trying to prepare an image of my simulated lipid bilayer structure obtained from
> sander/amber using a graphics program like VMD, but some molecules are always
> stretched out of the central box. This can not be solved by using "image" command in ptraj. The one way I can think of is that somehow one can get the image of the central box along with the neighboring boxes. Anyone has ideas how to do this or a better way?
>
> Thanks
>
> T.-X. Xiang
--
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NOTE: E-mail address has changed into
jongejan_at_few.vu.nl
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Aldo Jongejan
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands
e-mail: jongejan_at_few.vu.nl
tlf: +31 (0)20 4447612
fax: +31 (0)20 4447610
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Received on Mon Jan 27 2003 - 08:25:34 PST
