[AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large

From: Rana Rehan Khalid <ray.binm.gmail.com>
Date: Thu, 15 Jul 2021 16:32:49 -0400

Dear Amber users

I generated the mutant models (a dimer structure), Most of these mutant
models md runs are fine but some models failed during heating, I checked
the earlier threads
following things I have applied

1. I ran the annealing through pmemd.cuda and then also try it with sander
2. I also follow this thread http://archive.ambermd.org/201004/0189.html
3. I also used H++ to make my initial structure good. I also used the pqr
file of this complex. I thought maybe the initial structure was not good.

but facing the same error. My error is

vlimit exceeded for step 1; vmax = 74.4479

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 1059 805 804

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

I used this input file for heating

&wt type='TEMP0', istep1=0, istep2=9000, value1=0.0, value2=300.0 /
&wt type='TEMP0', istep1=9001, istep2=10000, value1=300.0, value2=300.0 /
&wt type='END' /

Kindly guide me how I can resolve this issue.

Thank you for your time in advance.

AMBER mailing list
Received on Thu Jul 15 2021 - 14:00:02 PDT
Custom Search