Thanks for the advice
Here're the test results
$ /Programs/amber11/test/jar
$ ./Run.jarz
diffing mdout.jar.save with mdout.jar
PASSED
$ /Programs/amber11/test/jar_multi
$ ./Run.jarz
This test must be run in parallel....skipping
On Jun 27, 2011, at 11:38 PM, Dwight McGee wrote:
> Hi,
>
> You can run the tests in $AMBERHOME/test/jar and $AMBERHOME/test/jar_multi
> in order to check it.
>
> On Mon, Jun 27, 2011 at 5:14 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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
>>>> AMBER.ambermd.org
>>>> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
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Received on Mon Jun 27 2011 - 15:00:06 PDT
