Hi Carlos,
I've attached the full file. The end of it reads:
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
Thanks,
Amy
-----Original Message-----
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Wednesday, April 14, 2021 11:02 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] .rst file not produced during production run
what did the end of the wat_md.out file say?
On Wed, Apr 14, 2021 at 12:51 PM Roberts, Amy L2 <AMY.ROBERTS.ucdenver.edu>
wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 16 2021 - 12:30:03 PDT
