Hi,
I think it would help if we knew more about the trajectory itself and
how it was generated. Is this from a single MD run? What did you MD
input file look like? Also, could you possibly attach your complete
output from cpptraj? This will give us a few more details on your
topology/trajectory that may help to figure out what is going on.
Thanks,
-Dan
On Tue, Jun 3, 2014 at 7:46 AM, Soumendranath Bhakat
<bhakatsoumendranath.gmail.com> wrote:
> Hii;
>
> Please attach pdbs corresponding to 2s, 5s, 6s, 7s, 10s, 21s, and 22s using
> CPPTRAJ outtraj command. Attach those pdbs. Then we can see.
> Command for dumping PDB
>
> trajin md2.mdcrd
> autoimage
> strip :WAT,Na+ outprefix stripped
>
> outtraj snapshot.pdb onlyframes 30000 (put 2000 for 2ns, 5000 for 5ns, 6000
> for 6ns here)
>
> trajout md2_dry.mdcrd
>
>
> On Tue, Jun 3, 2014 at 3:23 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Tue, Jun 3, 2014 at 2:43 AM, yjlee <yjlee.apctp.org> wrote:
>>
>> > Thank you, Jason. Now I installed ambertools14 and autoimage command
>> > works well.
>> >
>> >
>> > Still I have the same problem. I transformed the rst files into pdbs,
>> > using
>> > CPPTRAJ with autoimage command, and checked the result with VMD.
>> >
>> > Here's the script that I used which saved as ####.inp
>> > trajin /home/yjlee/cpptraj/rsts/NVTmd.rst_####
>> > autoimage
>> > trajout ./####.pdb pdb
>> >
>> > and I run CPPTRAJ as
>> > cpptraj ./purewater.prmtop ./1.inp
>> >
>> > the prmtop file is the same file that used for NVT simulation.
>> >
>> > So now I guess it's not imaging problem...
>> >
>> >
>> > Would anybody tell me what's the problem? Any suggestion would be
>> > appreciaited.
>> >
>> >
>> > *I re-write the youtube link for my simulation visualization. You would
>> > see the
>> > configuration change that I mean at (2s, 5s, 6s, 7s, 10s, 21s, and
>> > 22s).
>> >
>> > http://youtu.be/JpkKtBFTHEk
>>
>>
>> I'm assuming you are turning on periodic images in VMD. Try turning those
>> off. Just visualize the raw trajectory (of the one unit cell, without
>> imaging or anything) in VMD. Do you still see the apparent discontinuous
>> jumps?
>>
>> Also, what is your input file? There are plenty of options you can choose
>> that would make this appear to happen.
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
> _______________________________________________
> AMBER mailing list
> 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
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Received on Tue Jun 03 2014 - 07:30:02 PDT
