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
>
>
>
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>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Fri May 30 2014 - 02:30:03 PDT
