Actually I could find what might have caused the crash.
It's about the way how I created the input file for amber, that was in
my bash script in the following manner:
# print mpd file for production run without restraints at given temperature;
printf "*************************************************************************
***************************** md.in ******************************
*************************************************************************
MD without restraints during 20ns at constant T= "${i}"K & P= 1Atm
&cntrl
imin=0, ntx=5, ntpr=5000, ntwr=25000, ntwx=25000,
nscm=5000,
ntf=2, ntc=2,
ntb=2, ntp=1, taup=0.5,
nstlim=${md_production}, dt=0.002,
cut=10.0,
ntt=3, gamma_ln=2.0, ig=-1,
iwrap=1,
irest=1,
temp0=${i}.0
/
&ewald
netfrc = 0,
skin_permit = 0.75,
&end\n" > "${in_md}/md_production_${i}K.in"
Note I added \n just after the last &end, which was recognized as EOF.
Without such minor modification, it did not work. I remember 5 years
ago I used the same way of creating the inputs for GPU server that
worked fine without any modifications..
Il giorno ven 5 ago 2022 alle ore 15:26 Enrico Martinez
<jmsstarlight.gmail.com> ha scritto:
>
> Many thanks David!
> And do we actually need nscm=5000 using langevin dynamics like in my case?
> Cheers,
> Enrico
>
> Il giorno ven 5 ago 2022 alle ore 14:23 David A Case
> <david.case.rutgers.edu> ha scritto:
> >
> > On Fri, Aug 05, 2022, Enrico Martinez wrote:
> >
> > >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?
> >
> > First, be sure to check (e.g. visually) that your trajectory at 330K makes
> > good sense. There is no point in evaluating energies if something goes
> > wrong at this elevated temperature.
> >
> > Second, 50,000 snapshots is a lot for most mm-gbsa calculations. Consider
> > setting ntwx to 25,000 (say). You don't need to set ntwr -- that pretty
> > much just wastes time. And I don't think you need ntwe.
> >
> > Alternative: keep ntwx at 5000, but do an initial simulation for 100 ns,
> > rather than 500. See what you learn from the energies and fluctuations
> > for the shorter run. You can always do a longer run later.
> >
> > ....dac
> >
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Received on Mon Aug 08 2022 - 07:30:05 PDT
