Dear Adrian and Daniel,
Thanks a lot.. I really appreciate it !
I was wondering if you could review my control files to double check them
before starting over !
I have finished few introductory tutorials, and I encountered many errors
during this run. Please let me know if this possible !
Best Regards
On Tue, Aug 11, 2015 at 9:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Tue, Aug 11, 2015 at 12:46 PM, Adrian Roitberg <roitberg.ufl.edu>
> wrote:
> > Sorry to tell you , but you have a bigger problem. You are using the
> > internal random seed for the langevin thermostat, while you should be
> > using ig=-1
>
> For more information see http://pubs.acs.org/doi/abs/10.1021/ct8002173.
>
> >
> > I would not trust your results and would start over, using ig=-1 AND
> > iwrap=1. Also, if you have netcdf, use ioutfm=1
> >
> > adrian
> >
> >
> > On 8/11/15 1:18 PM, Amber mail wrote:
> >> Dear AMBER users,
> >>
> >> Wish you are fine
> >>
> >> I performed a 80 ns MD simulation in 8 stages, using AMBER12, each stage
> >> for 10 ns.
> >>
> >> *Description of the simulation:*
> >>
> >> I used this md control file for all stages
> >>
> >> Production
> >> &cntrl
> >> imin=0,
> >> ntx=5,
> >> irest=1,
> >> nstlim=5000000,
> >> dt=0.002,
> >> ntf=2,
> >> ntc=2,
> >> temp0=310.0,
> >> tempi=310.0,
> >> ntpr=5000,
> >> ntwx=5000,
> >> cut=8.0,
> >> ntb=2,
> >> ntp=1,
> >> ntt=3,
> >> gamma_ln=1.0,
> >> /
> >>
> >> *The Error*:
> >>
> >> 70 ns MD simulation was performed without any problems, but the 8th
> >> stage(at 80 ns) failed due to this error below:
> >>
> >>> | ERROR: I could not understand line 8358
> >>> 56.2239165************-423.4551515
> 56.1995897************-423.0909738
> >>>
> >>> *s in the inpcrd file often indicate an overflow of the Fortran format
> used
> >>> to store coordinates in the inpcrd/restart files. This often happens
> when
> >>> coordinates are not wrapped into the center cell (when iwrap = 0) and
> some
> >>> particles diffuse too far away. Try restarting from your last good
> restart
> >>> file and setting iwrap=1 or using a NetCDF restart file format. See the
> >>> Amber manual for details
> >>> "mol500008.out" 58L, 3283C
> >>> 58,1 Bot
> >>>
> >>> I've checked the mailing list for a similar error, but It was not clear
> >> enough for me.
> >>
> >>
> >> *The question is:*
> >>
> >> Regarding the sentence from the mdout file, "Try restarting from your
> last
> >> good restart file ", how can I know how good the restart file is? does
> this
> >> simply mean a restart file from a completed stage?!
> >>
> >> Is the solution to this just by setting iwrap=1 and resume the 8th stage
> >> using the restart file from the 7th stage, or I have to repeat all the
> MD
> >> simulation with setting iwrap=1 ?!
> >>
> >> Does just setting iwrap=1 and resuming the simulation with the 8th stage
> >> affect the results of the MD simulation?
> >>
> >> I also want to point out that I managing to run the MD simulation till
> 100
> >> ns.
> >>
> >>
> >> Thanks in advance!
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > Dr. Adrian E. Roitberg
> > Professor.
> > Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> > 352-392-6972
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 11 2015 - 14:00:03 PDT
