VMD-L Mailing List

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Fri May 16 2008 - 09:42:20 CDT

Hi, Vlad-

Thanks for your reply!

I intended to use VMD to prepare the system outputting PSF and PDB files for
NAMD simulation. But if I use AMBER, can the output files be used as input
for NAMD simulation?

Thanks,
Yinglong

On Fri, May 16, 2008 at 4:29 AM, Vlad Cojocaru <
Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:

> Which program do you intend to use to create you truncated octahedron ? If
> its AMBER, please note that the vectors described by Gromacs won't work.
> If you do use AMBER to create your box, please check the AMBER mailing list
> archives ... this issue has been discussed there
>
> Best
> vlad
>
> George Madalin Giambasu wrote:
>
>> 1) Check out the Gromacs manual for how to specify the vectors of the unit
>> cell for the truncated oct.
>> 2) Make an estimate on how big the length of an edge of the oct. would be,
>> enter the values of the cell vectors in an Namd configuration file and let
>> your system equilibrate with NPT for a 1-2ns. Specify "wrapnearest on" and,
>> in the end, you will get truncated oct. shaped sytem.
>>
>> I hope this helps,
>>
>> George
>>
>>
>>
>>
> --
>
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>
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>
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-- 
Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981