Hi Adrian,
I have one VERY ROUGH data point: I merged two copies of a 4300 atom
protein, and it took about a week. I don't know exactly how long because I
forgot it was still running...I also know an undergrad working for me tried
to run the sidechain timerge tutorial and gave up after a couple days, in
case that's useful
Dan
On Thu, Mar 16, 2017 at 7:48 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Dear all
>
> We are having trouble using the timerge function in parmed.
>
> In particular, if we try to follow the tutorials A9 for a change in side
> chain, the system hangs for a long time.
>
> We are testing some smaller systems, and it seems that the scaling with
> system size is really bad.
>
> Can someone give us some idea abou how long one might expect the timerge
> to take vs system size ?
>
> thanks
>
> adrian
>
>
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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>
--
Daniel J. Mermelstein, Ph.D candidate
McCammon & Walker Groups
Department of Chemistry & Biochemistry
University of California, San Diego
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Received on Thu Mar 16 2017 - 16:00:03 PDT
