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/
>>
>> _______________________________________________
>> 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
>
>
--
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 - 01:00:03 PDT
