Thank you for your response and cares, Soumendranath.
As I understand, the CPPTRAJ script that you wrote convert one of the
frame written in the mdcrd file to pdb file, after taking the water
molecules and Na+ ions away, right?
I did similar thing, using restart file and PTRAJ program. It looks
like,
however, I still have the problem.
For my case, there are only water molecules so I didn't strip out
the water molecules. Also I have individual restart files for each
frames of NVT simulation.
Here's the PTRAJ script I used
trajin /home/yjlee/amber/purewater/rsts/NVTmd.rst_####
trajout ./####.pdb pdb
go
I did same thing, changing the #### to restart file name (which
corresponds
to the frame number) and loaded the pdb files with VMD. Still the
problem occurs.
ONE THING THAT CONCERNS ME IS the "autoimage" command in your script.
Since you
said it seems to be imaging problem, this command might be the
solution.
So I tried with your script, using CPPTRAJ, like this
trajin /home/yjlee/amber/purewater/rsts/NVTmd.rst_####
autoimage
trajout ./####.pdb pdb
but when I run the CPPTRAJ, I found that CPPTRAJ doesn't know
"autoimage" command.
[autoimage]
Warning: Unknown Command autoimage.
I couldn't find "autoimage" on ambertools manual file also.
Could you, anybody, give me some suggestion?
With many thanks,
yjLEE
> ------------------------------
>
> Message: 10
> Date: Fri, 30 May 2014 11:17:51 +0200
> From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
> Subject: Re: [AMBER] sudden and rapid configuration change in NVT
> simulation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CACF5Eq=cojCzhVfNW8wvwvNoYYAekJSb4KW9pGMO=4j5rfmPkw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hii;;
>
> Sorry I cant able to watch the video. But it seems to me it is
> imaging
> problem. Just a suggestion, take snapshot PDBs using CPPTRAJ and
> corresponds to the PDBs you see during visualisation. This imaging is
> a
> very common problem to visualise a simulation. If you think the same
> phenomena happens after taking snapshots using CPPTRAJ then provide
> the
> inputs during running.
>
> Script for taking snapshots
>
> trajin md2.mdcrd
> autoimage
> strip :WAT,Na+ outprefix stripped
>
> outtraj snapshot.pdb onlyframes 30000
>
> trajout md2_dry.mdcrd
>
> outraj will dump a pdb corresponding to 30,000 frame.
>
>
> Execute like ~/amber12/bin/cpptraj com_solvated.top snapshot.ptrj
>
>
> On Fri, May 30, 2014 at 10:44 AM, yjlee <yjlee.apctp.org> wrote:
>
>> Dear all amber users
>>
>> I'm doing NVT simulation with pure water system.
>> The system size is about 30 cubic Angstrom and there are about 800
>> water molecules.
>> The periodic boundary condition is applied to the simulation.
>>
>> POL3 watermodel was used.
>> I made the prmtop and inpcrd file using xleap, with
>> leaprc.ff02polEP.r1
>> file.
>>
>> I first did NPT simulation to get realistic water density,
>> and after that the NVT simulation was done.
>>
>>
>> The problem is, when I check the NVT result with visualization
>> program
>> (I use VMD),
>> I can see sudden and rapid configuration changes for whole system.
>>
>> I recorded the result and uploaded the video on youtube. Please
>> check
>> the video first.
>> ( http://youtu.be/JpkKtBFTHEk )
>>
>> Here the small triangles are watermolecules and the blue rectangular
>> box is unit cell.
>> The video is recorded in xy-plane, orthographical view.
>>
>> At 2sec, 5sec, 6sec, 7sec, 10sec, 21sec, and 22sec, you would see
>> what
>> I mean.
>>
>>
>> I first thought this might comes from the "nscm" option that removes
>> translational or
>> rotational move of center-of-mass, but after I set nscm = 0, still
>> it
>> happens.
>>
>>
>> Could anyone tell me why such chanages happen or how can I get the
>> result without that?
>>
>> I would really appreciate for any of your opinions.
>>
>>
>> Many thanks in advance,
>>
>> yjLEE
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
>
>
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Received on Mon Jun 02 2014 - 00:30:02 PDT
