Re: how obtain .xst form .dcd file?

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Mar 23 2011 - 14:11:27 CDT

Sure, just write a TCL loop that iterates over the frames with the right
step and write the info to a file. There are a lot of examples of such
scripts in the mailing list and in the VMD tutorial.

Best regards,
Ajasja

On Wed, Mar 23, 2011 at 18:59, wood irene <irewood_at_gmail.com> wrote:

> Thanks Erik,
> My .dcd has 2500000 steps and 2500 frames, and I must to obtain an .xst
> recorded every 10000 steps, that means that I must to get 250 times
> the dimensions of the simulation box. There is any alternative way two get
> the whole .xst file in only one step?
> Regards
>
> 2011/3/21 Erik Santiso <esantiso_at_mit.edu>
>
>>
>> Hi Irene,
>>
>> If there is unit cell information in the dcd file, you can get the unit
>> cell parameters with vmd. Just open the file with vmd and use molinfo get or
>> pbctools. With pbctools you'd do something like:
>>
>> package require pbctools
>> pbc get -namd
>>
>> That will give you the cell vectors. As far as I know, however, the origin
>> is not stored in the dcd file. Depending on what you want to do this may not
>> be important.
>>
>> Erik.
>>
>>
>> On 3/21/11 10:25 AM, wood irene wrote:
>>
>>> Dear all,
>>> could someone help me to get a .xst file from a .dcd file?
>>> thank in advance
>>> Irene
>>>
>>>
>
>
> --
> *Ire*
>

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