Re: [AMBER] problem restraint

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Thu, 11 Oct 2012 17:12:04 +0200

Ok thank you very much.

I read the correct number of atoms, but I have still some problems, but I
think they are not due to the program.

thanks a lot

Elisa

2012/10/11 Jason Swails <jason.swails.gmail.com>

> 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
> _______________________________________________
> 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
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Received on Thu Oct 11 2012 - 08:30:06 PDT
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