Re: [AMBER] problem restraint

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 11 Oct 2012 17:10:06 +0200

You would have to try it, I don't know for sure.

On Thu, Oct 11, 2012 at 4:51 PM, Elisa Frezza <elisa.frezza.gmail.com>wrote:

> Dear Jason,
>
> thank yo very much for your answer.
>
> Is it now right the input and the job script?
>
> run: step 1 MD
> &cntrl
> imin = 0,
> irest = 0 ,
> ntx = 1,
> nstlim = 5000, dt = 0.002,
> ntc = 2 , ntf = 2,
> ntt = 3, gamma_ln = 2.0,
> ntp=1, taup=1,
> pres0=1,
> tempi = 100.0, temp0 =100.0,
> ntb = 2 ,
> ntpr = 250 , ntwx = 250, ntwr = 500 ,
> cut = 9,
> ioutfm = 1
> ntr=1
> restraintmask = ':1-1516,
> restraint_wt=8000.0,
> &end
>
>
> cmd="pmemd.cuda.MPI -O -i step1.in -o dimero_step1.out -p
> dimero_spce.prmtop -c dimero_spce.
> inpcrd -r dimero_step1.rst -x dimero_step1.mdcrd -ref dimero_spce.inpcrd"
>
> export CUDA_NIC_INTEROP=1
>
> mpirun -np 4 $cmd
>
>
> thank you in advance
>
> Elisa
>
>
> 2012/10/11 Jason Swails <jason.swails.gmail.com>
>
> > On Thu, Oct 11, 2012 at 3:53 PM, Elisa Frezza <elisa.frezza.gmail.com
> > >wrote:
> >
> > > Dear all,
> > >
> > > I am using AMBER12 (pmemd.cuda.MPI) and I used the following input
> file:
> > >
> > > run: step 1 MD
> > > &cntrl
> > > imin = 0,
> > > irest = 0 ,
> > > ntx = 1,
> > > nstlim = 5000, dt = 0.002,
> > > ntc = 2 , ntf = 2,
> > > ntt = 3, gamma_ln = 2.0,
> > > ntp=1, taup=1,
> > > pres0=1,
> > > tempi = 100.0, temp0 =100.0,
> > > ntb = 2 ,
> > > ntpr = 250 , ntwx = 250, ntwr = 500 ,
> > > cut = 9,
> > > ioutfm = 1
> > > ntr=1
> > > &end
> > > Keep DNA fixed with weak restraints
> > > 8000.0
> > >
> >
> > Woah. These are HUGE restraints, that will almost certainly cause
> > integration errors (the SHAKEn H-heavy-atom bonds are over 10x lower than
> > this!)
> >
> > 'Weak' restraints are on the order of 1.0 - 2.0
> >
> >
> > Also, for Amber 12, consider using "restraintmask" and "restraint_wt"
> > instead of the GROUP input section (which is the part of the input file I
> > just interrupted).
> >
> > RES 1 136
> > > END
> > > END
> > > [snip]
> > > rfree: End of file on unit 5
> > >
> >
> > This suggests that the input file failed to be parsed when parsing the
> > group input, although I can't readily see why. But getting rid of the
> > group input should help.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Elisa Frezza
> Ph.D. Student in Materials Science and Engineering
> Dipartimento di Scienze Chimiche
> UniversitÓ di Padova
> via Marzolo, 1
> 35131 Padova - Italy
> Phone: +39 049 827 5149
> Skype: elisa.frezza
> Emai: elisa.frezza.gmail.com
> elisa.frezza.studenti.unipd.it
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Oct 11 2012 - 08:30:04 PDT
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