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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Received on Thu Oct 11 2012 - 08:00:03 PDT
