Re: [AMBER] by pmemd.cuda runs

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 31 May 2013 08:27:55 -0600

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
>> _______________________________________________
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>>
>>
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-- 
-------------------------
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)
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Received on Fri May 31 2013 - 07:30:04 PDT
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