Hi
You are specifying the creation of subimição command line file of the
simulation?
The following command line example for simulation in parallel:
mpirun -np 36 $AMBERHOME/bin/pmemd.MPI -i Min.in -o Min.out -p
HZY-LYC-RESP.prmtop -c HZY-LYC-RESP.inpcrd -ref HZY-LYC-RESP.inpcrd -r
Min.rst &
Best regards,
Marcelo A. Chagas
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2016-04-06 9:08 GMT-03:00 ABHIJEET CHOWDHURY <
f2013854.pilani.bits-pilani.ac.in>:
> Dear Amber users,
>
> I am trying to simulate a double stranded RNA but when I run the code
> no .rst file is created which I need for further simulation. (This is
> the fourteenth simulation run, there are 21.)
> equilibration
>
> &cntrl
>
> nstlim=50000, cut=12.0, ntr=1,
>
> ntpr=500, ntwr=10000, ntt=1, ntwx=5000, temp0=300.0, tempi =300.0,
>
> ntx=5, irest=1, scnb=2.0, scee=1.2,
>
> ntc=2, ntf=2, tol=0.00005,
>
> dt=0.002, ntb=0,tautp=2.0,
>
> nscm=500,
>
> igb=5, gbsa=1, saltcon=0.2,
>
> intdiel=1.0, extdiel=78.5,
>
> nrespa=4
>
> /
>
> Keep RNA except terminal ends fixed with weak restraints
>
> 80.0
>
> RES 2 21
> RES 24 43
>
> END
> Keep Terminal ends fixed with weak restraints
> 100.0
> RES 1
> RES 22 23
> RES 44
>
> END
> END
>
>
> I will appreciate if anyone can offer some suggestions.
> I am new to amber so please look for any basic mistakes first as the
> chances of committing some novice mistake is more probable.
>
> Abhijeet Chowdhury
> Student
> M.Sc.(Hons.) Biological Sciences
> B.E.(Hons.) Chemical Engineering
> Birla Institute of Technology and Science (BITS),
> Pilani 333 001, Rajasthan, INDIA
>
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Received on Wed Apr 06 2016 - 08:00:06 PDT
