Yes, setting the cut to 8.0 resolves this issue!
The command that now succeeds 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 per your suggestion I updated the contents of my 4_md.in to
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 8.0, 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
/
Thank you!
Amy
-----Original Message-----
From: David A Case <david.case.rutgers.edu>
Sent: Friday, April 16, 2021 3:01 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] .rst file not produced during production run
On Fri, Apr 16, 2021, Roberts, Amy L2 wrote:
>
>Cutoff list exceeds largest sphere in unit cell!!
> Big problems with imaging!!
> a,b,c = 24.047116319114011 22.573755462423588 27.547999941411810
> alpha,beta,gamma = 90.000000000000000 90.000000000000000 90.000000000000000
> cutlist,sphere = 11.287000000000001 11.286877731211792
You have a very small box size...very near the limit for Amber.
You need to reduce your cutoff for such a small cell. I'm guessing(?) that you set cut=9.287 in response to earlier messages like this. But with constant pressure, the cell size will decrease, and with it, the largest value of cut that you can use.
If this is "just" a student project, using the default cut of 8.0 should be fine for teaching. If you need to explore bigger cutoffs, you'll need to construct a bigger box.
....hope this helps...dac
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Received on Wed Apr 21 2021 - 14:30:02 PDT
