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
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Received on Fri May 31 2013 - 06:30:02 PDT
