Thanks Moth,
I set nscm to default values..
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: "Moth, Chris" <chris.moth.vanderbilt.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Friday, May 31, 2013 7:09 PM
Subject: Re: [AMBER] by pmemd.cuda runs
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 happened though... But looking at the actual numbers in the file could be interesting.
________________________________________
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)
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Received on Sat Jun 01 2013 - 03:30:04 PDT
