[AMBER] .rst file not produced during production run

From: Roberts, Amy L2 <AMY.ROBERTS.UCDENVER.EDU>
Date: Wed, 14 Apr 2021 16:51:07 +0000

Hello,

I'm trying to simulate a box of water as part of a student lab, but am finding that when I run the production step no .rst file is produced as output.

The command I am running is

$AMBERHOME/bin/sander -O -i 4_md.in -o wat_md.out -p wat.prmtop -c wat_equil.rst -r wat_md.rst -x water.mdcrd

And the contents of my 4_md.in are

&cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 9.287, ntr = 0,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 20000, dt = 0.001,
  ntpr = 100, ntwx = 1, ntwr = 1000
/

The minimization, defrost, and equilibration steps _seem_ to have gone according to plan.

Has anyone encountered an issue like this before? Is there additional information that would be useful for troubleshooting?

Thanks,

Amy

Assistant Professor of Physics
CU Denver | Downtown Campus

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Received on Wed Apr 14 2021 - 10:00:02 PDT
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