Re: [AMBER] sudden and rapid configuration change in NVT simulation

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Tue, 3 Jun 2014 15:46:30 +0200

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
>
>
> ‚ÄčI'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
Received on Tue Jun 03 2014 - 07:00:02 PDT
Custom Search