Hi Mark and Dan,
Thanks for responding..
The trajectory view seems wierd by chimera and vmd.
Nevertheless, pdb view of the last snapshot of 10 ns trajectory seems alright though.
As you suggested chimera and vmd visualization of the trajectories seems to be the problem...
Also energy values in md.out file seems alright..
Therefore, I centered the protein in the trajectory using ptraj and I am now able to view the entire trajectory with no problem..
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
________________________________
From: Marc van der Kamp <marcvanderkamp.gmail.com>
To: Cenk (Jenk) Andac <cenk_andac.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, May 31, 2013 4:12 PM
Subject: Re: [AMBER] by pmemd.cuda runs
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
>
>
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Received on Sat Jun 01 2013 - 03:30:03 PDT
