[AMBER] Minimization of a large water box

From: Sasha Buzko via AMBER <amber.ambermd.org>
Date: Sat, 6 Apr 2024 17:44:39 +0000

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 - 11:00:02 PDT