Re: [AMBER] problem restraint

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Thu, 11 Oct 2012 16:45:43 +0200

Dear Jason,

thank you very much for your answer.
Is it correct this input and 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 = ':1-119 & !.H=',
  restraint_wt=5.0,
  &end


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
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>



-- 
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 - 08:00:09 PDT
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