As Dave suggested, you should post your mdout file so we can see exactly
what was happening in the MD run.
On Fri, Jun 26, 2020 at 1:51 PM Erdem Yeler <erdemyeler.gmail.com> wrote:
> I changed the ntx parameter (as ntx=5) but nothing changed. I couldn't find
> my mistake. Any suggestions? Still I couldn't understand why my simulation
> looks like normal but energies are restarting at every 500 steps.
>
> Erdem Yeler <erdemyeler.gmail.com>, 12 Haz 2020 Cum, 19:49 tarihinde şunu
> yazdı:
>
> > Dear David, thanks for your help and reply. Here is my mdin file:
> >
> > &cntrl
> > imin = 0, irest = 1, ntx = 7,
> > ntb = 2, pres0 = 1.0, ntp = 1,
> > taup = 2.0,
> > cut = 10.0, ntr = 0,
> > ntc = 2, ntf = 2,
> > tempi = 300.0, temp0 = 300.0,
> > ntt = 3, gamma_ln = 1.0,
> > nstlim = 50000, dt = 0.0022
> > ntpr = 100, ntwx = 100, ntwr = 1000
> > /
> >
> >
> > David A Case <david.case.rutgers.edu>, 8 Haz 2020 Pzt, 03:31 tarihinde
> > şunu yazdı:
> >
> >> On Mon, Jun 08, 2020, Erdem Yeler wrote:
> >>
> >> > actually I couldn't find my mdin file. it was deleted by the
> >> >administrator of the server after the job was finished.But I copied all
> >> >files from the tutorial I mentioned above. I am doing multiple runs.
> >>
> >> I've lost track of what the "tutorial I mentioned above" is. Are you
> >> running separate jobs, each of 500 steps? It really sounds (as others
> >> have suggested) that somehow you are not updating the files correctly.
> >>
> >> If you have an mdout (output) file, the mdin file is listed at the top
> >> of that file. But we also need to know exactly what the command line
> >> arguments you are using. Those are also printed in the mdout file. So,
> >> examining carefully what is in the mdout file, and posting it if you
> >> can't find anything wrong, might be the next step.
> >>
> >> ...dac
> >>
> >>
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Received on Fri Jun 26 2020 - 11:30:03 PDT
