Thank you very much David!
I will check everything and then report to you.
Regarding your last comment, in fact I've just changed the duration of
the simulation by increasing the number of steps producing a
trajectory of 500 ns. Assuming that the aim is to calculate dG of the
ligand binding using MMGBSA approach, what values should be reasonable
for ntpr=5000, ntwr=5000, ntwx=5000, ntwe=5000, nscm=5000?
Many thanks in advance
Cheers
Enrico
Il giorno gio 4 ago 2022 alle ore 18:56 David A Case
<david.case.rutgers.edu> ha scritto:
>
> On Thu, Aug 04, 2022, Enrico Martinez via AMBER wrote:
>
> >I've noticed that I always got a crush with the Fortran error in the
> >case of the execution of the input file with the following options
> >used to run job with GPU:
> >
> >*************************************************************************
> >***************************** md.in ******************************
> >*************************************************************************
> >MD without restraints during 20ns at constant T= 330K & P= 1Atm
> > &cntrl
> > imin=0, ntx=5, ntpr=5000, ntwr=5000, ntwx=5000, ntwe=5000,
> > nscm=5000,
> > ntf=2, ntc=2,
> > ntb=2, ntp=1, taup=0.5,
> > nstlim=250000000, dt=0.002,
> > cut=10.0,
> > ntt=3, gamma_ln=2.0, ig=-1,
> > iwrap=1,
> > irest=1,
> > temp0=330.0
> > /
> > &end
> > &ewald
> > netfrc = 0,
> > skin_permit = 0.75,
> >&end
> >
> >I could fix it via adding an empty line after the last &end. Could it
> >be related to my particular system or is it a bug of the amber22?
> >Many thanks in advance
>
> It's very hard to debug something like this without seeing the input file that
> failed as an attachement. It's possible that there is no end-of-line on the
> final line. Or something else might be happening. A couple of things to try:
>
> 1. At the end of the &cntrl namelist, you have both a "/" and an "&end"
> statement. The latter is quite obsolete, although most compilers still allow
> it. I don't think this is causing a problem but you might as well get used
> to using "/"
>
> 2. You are actually asking for 500 ns of simulation, not 20 ns as the comment
> suggests. And you will have 50,000 entries in your mdout, mden and trajectory
> files, plus write a restart file 50,000 times. Make sure your project really
> requires such fine-grained sampling.
>
> .....dac
>
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Received on Fri Aug 05 2022 - 01:30:03 PDT
