Re: how to convert dcd files from namd to charmm

From: regafan_at_usc.es
Date: Thu Mar 15 2007 - 09:56:03 CDT

Thank you very much, Alessandro.
You were right, I had run NAMD on a computer of different endianness
of the computer on which I was analyzing the trajectory with Charmm.
Now, it works without any format conversion.
Thanks!

Rebeca García
Post-doctoral student
Barcelona
Spain

Citando Alessandro Cembran <cembran_at_chem.umn.edu>:

> Rebeca,
>
> I've been running NAMD and post processing the trajectories with CHARMM
> as well and I've never run into any problem.
> In some cases, one might have to pay attention to the orientation of
> the box (I am thinking about hexagonal cells, that need to be rotated
> by 15 degrees around the Z axis) but the raw numbers are always read
> correctly.
> Another thing that I can think of is that you might have run NAMD on a
> computer of different endianness of the computer on which you are
> analyzing the trajectory. If this is the case, you might
> a) Recompile CHARMM with TESTENDIAN in the pref.dat (never tried this one)
> b) Change the endianness of the shell on which you are running CHARMM
> to match the original one:
> export F_UFMTENDIAN=little or ...=big
> c) Compile and run CHARMM on the machine the trajectories have been produced.
>
> If none of the two cases applies to your problem, then could you be
> more specific about what is the compatibility issue?
>
> Alessandro
>
> regafan_at_usc.es wrote:
>> Hello,
>> I have done a simulation of a protein with NAMD, using the Charmm
>> force field, and now I would like to perform an analysis with CHARMM.
>> I have problems of compatibility of the trajectory files obtained
>> with NAMD and CHARMM. Does anyboy knows how to convert a dcd
>> trajectory file from NAMD to the correct one used by Charmm?
>>
>> Thanks a lot!
>>
>> Rebeca García
>> Post-doctoral student
>> Barcelona
>> Spain
>>
>>
>
>
> --
> Alessandro Cembran,PhD
> Post Doctoral Associate
> Mailing Address:
> Univ. of Minnesota, Dept. of Chemistry
> G2, 139 Smith Hall 207 Pleasant St SE
> Minneapolis, MN 55455-0431
> Office:
> Univ. of Minnesota, Walter Library
> 117 Pleasant St SE, Room 473
> Phone: +1 612-624-4617
> E-mail: cembran_at_chem.umn.edu

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