Hi,
On Sun, May 25, 2014 at 4:50 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> 1) Does it possible to re-start previously manually terminated simulation
> (using restr file) and write trajectory in the existing .crdbox file
> preventing creation of new one for restarting run?
I would recommend against doing this. For one thing it is too easy to
make a mistake and accidentally overwrite something important.
Subsequent trajectory analysis won't care if you have separate
trajectories anyway, and if for some reason you just want everything
in one trajectory file you can always combine them later with cpptraj.
> 2)More specified question: I need to calculate number of water molecules
> which are within selected cutoff distance or radius to the selected protein
> residue along my trajectory. I've found some VMD scripts for this task but
> it has shown wrong (mainly overestimated) results (this time I've analyzed
> dcd trajectory created from the amber's crdbox). I'll be very thankful if
> someone also have faced with the same problem and has some script for such
> task.
Check out the 'watershell' command in cpptraj.
-Dan
>
> TFH,
> James
>
>
> 2014-05-22 17:22 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
>
>> On Thu, 2014-05-22 at 16:52 +0400, James Starlight wrote:
>> > When I've tried to convert my amber 100ns trajectory to dxd using cpptraj
>> > it took about 1 hour :) Does catDCD or any other terminal utilities can
>> do
>> > such tasks?
>>
>> This sounds like a filesystem issue. You can also look into mdconvert
>> (part of the MDTraj Python suite) available here:
>> http://mdtraj.org/latest/
>>
>> Or you can use VMD (which uses catDCD, I believe). I believe the DCD
>> reading/writing code from MDTraj uses the VMD plugin (which, like I
>> said, is the same as catDCD, I think). When I tested cpptraj and
>> mdconvert on my machine with a 22K atom system with a 6.9 GB trajectory
>> (100 ns), cpptraj took 53 seconds and mdconvert took 51 seconds.
>> >
>> > By the way also I have a question about proper loading of the
>> trajectories
>> > to the VMD
>> >
>> > e.g using
>> > vmd ionized.prmtop md.mdcrd
>> >
>> > VMD recognize this trajectory as without PB box. Does it possible to fix
>> it
>> > providing some flag to VMD?
>>
>> vmd -parm7 ionized.prmtop -crdbox md.mdcrd
>>
>> Other helpful flags for VMD:
>>
>> -netcdf <netcdf file> (.nc)
>> -crd <amber mdcrd without box> (.mdcrd, .crd)
>> -rst7 <amber inpcrd or restart file> (.rst7)
>>
>> In parentheses are the filename extensions that are autodetected (and
>> therefore don't need the flag)
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
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>>
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--
-------------------------
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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Received on Tue May 27 2014 - 07:00:02 PDT
