Hi James,
VMD does that (see command "animate write dcd")
Best,
Vlad
On 05/21/2014 05:19 PM, James Starlight wrote:
> Thanks Dan!
>
> Could someone suggest me some unix utility useful for the conversion of the
> amber's trajectory format to the charm-like .dcd ?
>
> James
>
>
> 2014-05-20 19:57 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> Hi,
>>
>> On Tue, May 20, 2014 at 9:05 AM, James Starlight <jmsstarlight.gmail.com>
>> wrote:
>>> Firstly I'd like to know about possibility to generate *.rest file
>>> (consisted of coordinates +felicitates +box vectors in specified time
>> step)
>>> from selected step of the output trajectory or md.out file. For instance
>>> one of my recent simulations have been crashed and broken check point
>> file
>>> have been created so I'd like to restore it manually.
>> You can restore coordinates from a trajectory file, e.g.
>>
>> trajin input.nc 30 30 # selects frame 30 only
>> trajout restart.rst7
>>
>> but unless you were also writing velocities (i.e. ntwv != 0) you
>> cannot create a true restart file. If you have a separate velocity
>> trajectory you can use those velocities with the 'mdvel' keyword, e.g.
>>
>> trajin input.nc 30 30 mdvel vel.nc
>>
>> or if you wrote a combined coordinate/velocity trajectory (NetCDF
>> only) the velocities will be read in automatically.
>>
>> You can generate random starting velocities for a new MD run according
>> to a temperature distribution by running with irest=0, ntx=1, and
>> ig=-1.
>>
>> Hope this helps,
>>
>> -Dan
>>
>>> James
>>> _______________________________________________
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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Wed May 21 2014 - 08:30:02 PDT
