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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 18 2013 - 09:30:03 PDT
