Nice catch !!
I am now using default nscm values and set ioutfm to 1 .
Thank you!!
Cenk Andac, M.S., Ph.D.
Asst. Professor of Medical Pharmacology
Department of Medical Pharmacology
School of Medicine, Mevlana University, Konya
Turkiye 42003
Cell: +90-(536)-4813012
E-Mail:cenk_andac.yahoo.com
Web : http://med.mevlana.edu.tr/personel.asp?ID=1
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Friday, May 31, 2013 9:11 PM
Subject: Re: [AMBER] by pmemd.cuda runs
On Fri, May 31, 2013 at 12:09 PM, Moth, Chris <chris.moth.vanderbilt.edu>wrote:
> With nscm=0, isn't it possible for translational motion to drive the
> coordinates outside of those which
> can be represented in an ASCII restart file format?
> Seems like a short time-frame for that to have hap
>
> pened though... But looking at the actual numbers in the file could be
> interesting.
>
Good catch. nscm=0 is dangerous in implicit solvent, since stuff diffuses
away very quickly (especially if the system picked a little bit of net
translational momentum -- it would fly away and never come back!)
Check the ASCII trajectory for ***s or other such strange values. In the
future, let nscm stay at its default value and use "ioutfm=1" to use NetCDF
trajectories (they're better in almost every way).
HTH,
Jason
>
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Friday, May 31, 2013 9:27 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] by pmemd.cuda runs
>
> Hi,
>
> Just to add to the above advice, one way to tell if there is a visual
> artifact or your system really is "out of shape" is to look at the
> energies reported in MDOUT. If you see a big jump around 7.5 ns this
> could be a real issue, otherwise my guess is there is something
> strange going on with the visualization.
>
> -Dan
>
> On Fri, May 31, 2013 at 7:12 AM, Marc van der Kamp
> <marcvanderkamp.gmail.com> wrote:
> > Hi,
> >
> > >From the image you attached, I am guessing this is an issue with the way
> > you view your protein structure rather than with the simulation. It
> appears
> > that for some atoms, the coordinates read in by your visualization
> program
> > (VMD?) are strange - really far away from the other atoms.
> > (This would be almost impossible to occur in simulation.)
> >
> > How are you viewing your protein, i.e. what format do you load and how?
> > Perhaps try writing a pdb file using ptraj or cpptraj and load that.
> >
> > --Marc
> >
> > On 31 May 2013 13:32, Cenk (Jenk) Andac <cenk_andac.yahoo.com> wrote:
> >
> >> Dear Amber users,
> >>
> >> I have been recently working on a protein simulation using the GB
> implicit
> >> solvent model (with igb=8),
> >>
> >> I used the following input parameters
> >>
> >> pmemd.cuda input
> >> &cntrl
> >> imin=0,irest=1,ntx=5,
> >> nstlim=500000,dt=0.002,ntb=0,
> >> ntf=2,ntc=2,tol=0.000001,
> >> ntpr=2500, ntwx=2500, ntwr=2500,
> >> cut=9999.0, rgbmax=9999.0,
> >> igb=8,ntt=0,nscm=0,
> >> /
> >>
> >> For the first 7 ns of the simulation everything seems OK. However, after
> >> 7.5 ns of the simulation the protein seems to bend out of shape as seen
> in
> >> the attached file.
> >> I also noticed that the protein system seems to move out of the screen
> ..
> >>
> >> I plan on centering the molecule during MD runs. Before doing that
> >> I just want to make sure that the prameters above are alright..
> >>
> >> Any ideas about what might be going wrong here ?
> >>
> >> Regards,
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Cenk Andac, M.S., Ph.D.
> >>
> >> Asst. Professor of Medical Pharmacology
> >> Department of Medical Pharmacology
> >> School of Medicine, Mevlana University, Konya
> >> Turkiye 42003
> >>
> >>
> >> Cell: +90-(536)-4813012
> >> E-Mail:cenk_andac.yahoo.com
> >> Web : http://med.mevlana.edu.tr/personel.asp?ID=1
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> > _______________________________________________
> > 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) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
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>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Jun 01 2013 - 03:30:03 PDT
