OK, thank you Dan!
Elisa
Il 08/set/2017 20:09, "Daniel Roe" <daniel.r.roe.gmail.com> ha scritto:
> Hi,
>
> Unfortunately you can't really restart this replica run because you've
> effectively lost a member of the ensemble. You should just start with
> a new initial set of velocities (i.e. use irest=0).
>
> -Dan
>
> On Fri, Sep 8, 2017 at 8:43 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
> > Hello,
> >
> > I have a problem in restarting pH-REMD simulations. My calculations were
> > killed for a hardware problem, and now I have to restart them. But I
> guess
> > the calculations stopped right during the writing the rst7 files, because
> > when I tried to restart using them, I got:
> >
> > begin time read from input coords = 20280.000 ps
> >
> >
> > | ERROR: Duplicate pHs in pH-REMD
> >
> > because actually 5 out of 6 replicas are restarting from time=20300.000
> ps,
> > while 1 of them is restarting from time=20280.000 ps. I (childishly
> maybe)
> > then tried to restart all of them from time=20280.000 ps, by writing out
> > the corresponding frame from the nc files. What I get now is:
> >
> > | ERROR: I could not find enough velocities in ph4.5.rst7
> >
> > So obviously I'm missing a way to write the velocities in those rst7
> files.
> > Is this the way to proceed to restart my simulations? Or is there a
> better
> > way?
> >
> > I hope I made my problem understandable.
> > Thank you!
> >
> > Elisa
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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Sat Sep 09 2017 - 01:30:02 PDT
