Re: [AMBER] Steered Molecular Dynamics

From: George Tzotzos <gtzotzos.me.com>
Date: Mon, 27 Jun 2011 23:14:39 +0200

Thanks Adrian,

I run sander as per your suggestion ntpr=1, ntwx=1, ntwr=1

sander -O -i smd.in -o smd.out -p 2wc6_bom_solv.prmtop -c prod.rst -r smd.rst -x smd.mdcrd

I still get segmentation fault. The output file is attached.

I don't recall getting any error messages during installation. Can you please point to me how to check jar?

Thanks again

George







On Jun 27, 2011, at 10:58 PM, Adrian Roitberg wrote:

> Hi,
>
> a couple of things to try.
>
> Set nstlim to 100 and
> ntpr=1000, ntwx=1000, ntwr=5000
>
> all to 1 or 10, so you have a fighting chance to see something in the
> output.
>
> Second (perhaps first!): do the jar tests cases pass ?
>
> Adrian
>
>
> On 6/27/11 10:40 PM, George Tzotzos wrote:
>> For both cases:
>>
>> 1. sander -O -i smd.in -o smd.out -p 2wc6_bom_solv.prmtop -c prod.rst -r smd.rst -x smd.mdcrd
>>
>> 2. mpirun -np 12 sander.MPI -O -i smd.in -o smd.out -p 2wc6_bom_solv.prmtop -c prod.rst -r smd.rst -x smd.mdcrd
>>
>> I get a smd.out which I'm attaching for diagnostics.
>>
>> Best regards
>>
>> George
>>
>>
>>
>>
>>
>>
>>
>> On Jun 27, 2011, at 10:06 PM, Dmitry Nilov wrote:
>>
>>> Hello,
>>> I am not sure that it is possible to perform SMD by pmemd. Try to use
>>> sander.MPI instead of pmemd.MPI.
>>>
>>> On Mon, Jun 27, 2011 at 9:49 PM, George Tzotzos<gtzotzos.me.com> wrote:
>>>> Hi everybody,
>>>>
>>>> I've just completed a 10ns production run of a protein-ligand complex. I would like to study the dissociation of this complex and fI thought that SMD would be suitable for this purpose. I tried to repeat the process described in the Amber 11 manual as well as in this website (http://enzyme.fbb.msu.ru/Tutorials/Tutorial_3/).
>>>>
>>>> I've started sander from a directory containing the solvated prmtop file, the trajectory from the production run and a distance restraint file.
>>>>
>>>> When I run
>>>>
>>>> mpirun -np 12 pmemd.MPI -O -i smd.in -o smd.out -p 2wc6_bom_solv.prmtop -c prod.rst -r smd.rst -x smd.mdcrd
>>>>
>>>> I get
>>>>
>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
>>>>
>>>> smd 2wc6-bombykol
>>>> &cntrl
>>>> imin=0,irest=1,ntx=5,
>>>> nstlim=500000,dt=0.002,
>>>> ntc=2,ntf=2,
>>>> cut=8.0, ntb=2, ntp=1, taup=2.0,
>>>> ntpr=1000, ntwx=1000, ntwr=5000,
>>>> ntt=3, gamma_ln=2.0, ig=-1,
>>>> temp0=300.0,
>>>> jar=1,
>>>> /
>>>> &wt TYPE='DUMPFREQ', istep1=1, /
>>>> &wt TYPE='END', /
>>>> DISANG=dist.RST
>>>> DUMPAVE=dist_vs_t
>>>> LISTIN=POUT
>>>> LISTOUT=POUT
>>>>
>>>> and the distance restraint dist.RST
>>>>
>>>> # Change distance restraint between atoms
>>>> &rst iat=1533,2223, r2=2.0, rk2=1.0725, r2a=8.0 /
>>>>
>>>> where 1533 and 2223 are atom numbers derived from the pdb file.
>>>>
>>>> Any help would be much appreciated.
>>>>
>>>> Regards
>>>>
>>>> George
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Dmitry Nilov
>>> Faculty of Bioengineering and Bioinformatics,
>>> Lomonosov Moscow State University
>>> web: http://enzyme.fbb.msu.ru/
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> Full Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



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Received on Mon Jun 27 2011 - 14:30:03 PDT
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