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
