Do you get any output at all? Try reducing maxcyc to 10 or less to see if
it finishes. That number of waters should not cause failure.
On Sat, Apr 6, 2024, 1:45 PM Sasha Buzko via AMBER <amber.ambermd.org>
wrote:
> Dear All,
> I'm trying to minimize a fairly large octahedral OPC water box with the
> total number of waters that can be between 100k and 250k. As it gets
> larger, the pmemd minimization (predictably) starts taking longer but then
> eventually stops finishing at all and produces no useful output to diagnose
> the issue.
> The input looks like this:
> &cntrl
> imin = 1, maxcyc = 1000,
> ncyc = 20, ntx = 1,
> ntwe = 0, ntwr = 10, ntpr = 10,
> ntc = 2, ntf = 2, ntb = 1, ntp = 0,
> cut = 10.0,
> ntr=1, restraintmask = ':1-618',
> restraint_wt = 100.,
> ioutfm=1, ntxo=2,
> /
>
> Is there anything that may need to be modified in the input to accommodate
> the large number of waters? Do you know if there is a hard-coded cutoff for
> a number of waters that may be in the system?
>
> Thank you in advance
>
> Sasha
>
>
> ---
> Oleksandr "Sasha" Buzko
> Computational Biology
> ImmunityBio
> 9922 Jefferson Blvd
> Culver City, CA 90230
>
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Received on Sat Apr 06 2024 - 12:00:02 PDT
