Hi Jason,
Thanks for the quick reply and the suggestion about the cutoff. But I
would like to bring to your attention that I have a simple protein
(basically a single protein, not a complex). Although I tried to run the
simulation with a higher cut-off as you suggested, the error massage is
again the same that I posted in my previous mail and eDo you have ventually
the job stops. Do you have any comment on this? Shall I modify or do some
additional stuffs here?
I would be really grateful if you can help me in this regard.
Thanking you,
Regards
Aditya.
On Tue, Jun 18, 2013 at 9:44 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Jun 18, 2013 at 11:32 AM, Aditya Padhi <adi.uoh.gmail.com> wrote:
>
> > Dear Amber users,
> > I am trying to run a simulation using implicit solvent with
> ff99sb
> > force field. When I submit the job, after some time it shows the
> following
> > error:
> >
> > | MPI Timing options:
> > | profile_mpi = 0
> > | INFO: Old style inpcrd file read
> >
> >
> >
> >
> --------------------------------------------------------------------------------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> >
> --------------------------------------------------------------------------------
> >
> > and the job stops. I looked for suggestions in the mailing list, where
> some
> > people have already faced these problems. I looked at the following link
> > http://structbio.vanderbilt.edu/archives/amber-archive/2009/1529.php and
> > found that in my .rst file also, there is a streth of ********* lines.
> But
> > as it is an implicit solvent simulation, I can not use ntb=1 and iwrap=1.
> > My input file is as follows:
> >
> > zed Born, 12 angstrom cut off
> > &cntrl
> > imin = 0, ntb = 0
> > igb = 5, alpb=1, ntpr = 2500, ntwx = 2500,
> > ntt = 3, gamma_ln = 1.0,
> > tempi = 300.0, temp0 = 300.0
> > nstlim = 15000000, dt = 0.002,
> > cut = 12.0
> > /
> >
>
> For implicit solvent, a 12 Angstrom cutoff is likely too small. My
> suggestion is to use a cutoff >= 1000 (effectively no cutoff).
>
>
>
> >
> > Please let me know that could be the solution for this or am I doing any
> > mistakes in the input file.
> >
>
> This typically happens if your system is composed of two different
> 'molecules' and they diffuse very far away from one another. There is no
> unbiased 'fix' for this -- you can add a restraining potential to prevent
> this kind of diffusion, but more likely this situation indicates the
> weaknesses of GB for your system if you know the complex to be stable.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Tue Jun 18 2013 - 11:30:03 PDT
