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

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 5 Jun 2014 08:40:17 -0400

On Thu, Jun 5, 2014 at 7:47 AM, yjlee <yjlee.apctp.org> wrote:

> Thank you so much for your concerns and comments, Jason, Soumendranath,
> and Daniel!
>
>
> > Do you still see the apparent discontinuous jumps?
> YES, it still happens when I turn OFF periodic boundary condition.
> Actually the reason that I turned on pbc in VMD was to show that the
> problem is not pbc problem...
>
> > Also, what is your input file?
> I use the PRMTOP file and RESTART files that recorded for every [ntwr]
> steps.
> For my case, [dt = 0.001] and [ntwr = -4] so new restart files were
> created for every 4 steps(0.004ps).
>
> > Please attach pdbs corresponding to 2s, 5s, 6s, 7s, 10s, 21s, and 22s
> > using CPPTRAJ outtraj command.
> > Also, could you possibly attach your complete output from cpptraj?
> I'll send you the files, by writing mail directly to you.
> (I'm new on amber mailing list. Is it possible to send file of ~10MB
> size via this mailing service?)
>
>
> > Is this from a single MD run?
> I don't clearly understand what you mean by "single".
> Here I write the steps I did. This information might be help...
>
> 0. I made prmtop and inpcrd file with xleap.
> 1. energy optimization [imin = 1] was done
> 2. I did heating up process and made the system temperature as 300K
> 3. NPT simulation was done to make the realistic water density (around
> 1)
> 4. NVT simulation was done
>
> I visualized the NVT simulation result with VMD.
> (which you can check with youtube video, http://youtu.be/JpkKtBFTHEk )
>
>
> > What did you MD input file look like?
> Here I write the input file I used for NVT simulation.
>
> purewater : NVT simulation
> &cntrl
> imin = 0,
> ntx = 5,
> irest = 1,
> iwrap = 1,
> ntr = 0,
> nstlim = 12000, dt = 0.001,
> nscm = 0
> ntt = 3,
> temp0 = 300.0,
> ig = -1,
> gamma_ln = 1.0,
> ntc = 2,
> ntf = 2,
> ntb = 1,
> cut = 6.0,
>

‚ÄčThis cutoff is way too short. You should be using at least 8 A.
‚Äč

> ipol = 1,
>

Are you _sure_ that you are using a polarizable water model? Even if you
are, the current versions of Amber set the ipol flag in the topology file.
 You should get rid of this variable from your input file.

In general, you can't just "turn on" polarizability for any force field.
 You must select a polarizable force field.

    ntpr = 4,
> ntwx = 4,
> ntwr = -4

   /
> END
>
>
>
> Thank you very much for your concerns and comments.
>
> Many thanks in advance,
>
> yjLEE
>
>
>
>
>
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Date: Tue, 3 Jun 2014 08:12:07 -0600
> >
> >
> > 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
> > (801) 585-6208 (Fax)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 05 2014 - 06:00:02 PDT
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