Try to set r2=4.818 in dist.RST.
As I understand, tests in /test/jar are passed. Inspect all outputs in
/test/jar. If they seem ok I just suggest that some of your input
files can be corrupted.
On Tue, Jun 28, 2011 at 12:40 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Dmitri
>
> A dist_vs_t file was produced. It was a single line
>
> 2.00000
>
> Thanks
>
> George
>
>
> On Jun 28, 2011, at 9:34 AM, Dmitry Nilov wrote:
>
>> It seems that the initial reference distance R2 = 2.000 while
>> initial actual distance Rcurr = 4.818. So the difference is
>> considerable that leads to large force. Did you get dist_vs_t output
>> file?
>>
>> On Tue, Jun 28, 2011 at 12:40 AM, George Tzotzos <gtzotzos.me.com> 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/
>>>>
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
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>>> 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
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
web: http://enzyme.fbb.msu.ru/
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Received on Tue Jun 28 2011 - 02:30:05 PDT
