Re: [AMBER] Coordinate resetting (SHAKE) can not be accomplished

From: Ahmed Elrashedy <ahmedelrashedy45.gmail.com>
Date: Tue, 17 Sep 2019 09:30:29 +0200

Dear Sunita

*Exceeded vlimits are generally indicative of overlapping atoms. Try
**printing
to your trajectory every step for a small number of steps *
*(ntwx=1) and visualizing the result to see if you can tell which atoms **may
be causing the problems. *

*You may try minimizing and carefully heating the system in order to **relieve
those bad contacts. However, it you have already run some *
*some MD and this run is a restart, so you **should probably set the
variables "irest=1, ntx=5". Also, if you want **to run with a 0.002
timestep, you should be SHAKEing bonds involving **hydrogen atoms d**o this
with "ntf=2, ntc=2". *

sincerely
Ahmed



On 17 Sep 2019 08:35, "Sunita Patel" <sunita.patel.cbs.ac.in> wrote:

Dear Amber users,
We started the simulation using AMBER18 and ff14IDPSFF force field. After
about 20 ps I got following message saying 'Coordinate resetting (SHAKE)
can not be accomplished'. Pls have a look on the message below.

What could be the problem for this?

Sincerely,
Sunita

-------------------------------
 NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 298.80 PRESS =
369.3
 Etot = -43728.9578 EKtot = 10530.7031 EPtot =
 -54259.6609
 BOND = 279.3889 ANGLE = 751.5951 DIHED =
 1156.6750
 UB = 0.0000 IMP = 0.0000 CMAP =
 -124.8653
 1-4 NB = 313.5412 1-4 EEL = 3152.8896 VDWAALS =
 6922.7743
 EELEC = -66711.6599 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 4764.3495 VIRIAL = 3364.6919 VOLUME =
 175528.0018
                                                    Density =
1.0039
 Ewald error estimate: 0.2475E-03
 ------------------------------------------------------------------------------

vlimit exceeded for step 10225; vmax = 1192.6561

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 334 685 686

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
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Received on Tue Sep 17 2019 - 01:00:02 PDT
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