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
With thanks,
yjLEE
> You must be using a very old version of cpptraj. Upgrade to the
> latest
> AmberTools release.
>
> Also, if you don't want waters (or ions) in your PDB file, you need
> to
> strip those out using the "strip" command. All of this described in
> the
> latest Amber 14 manual (that comes with the AmberTools 14 download).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>> From: yjlee <yjlee.apctp.org>
>> Date: Mon, 02 Jun 2014 15:47:17 +0900
>>
>>
>> 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 Tue Jun 03 2014 - 00:30:02 PDT
