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 Fri Sep 08 2017 - 11:30:02 PDT
