Hello Amber community,
I am using Amber's NFE module for doing some steered MD. I have implemented
a new collective variable that represents the binding between two residues
of a salt bridge and the translation of one of them relative to a third
residue. The code compiles without errors and a SMD simulation starts as
expected. However, after a few ten thousand steps the vlimit is exceeded. I
suppose this error is because of the new collective variable because
simulations with other collective variables work fine. I am trying to find
out what is the most likely reason for this error. Can it be related to how
the gradient is calculated? Maybe it gets too steep? Any help would be
appreciated.
Thanks!
Georg
Here are the last lines from the mdout file:
NSTEP = 71000 TIME(PS) = 205242.000 TEMP(K) = 309.94 PRESS =
0.0
Etot = -112213.8769 EKtot = 53399.5438 EPtot =
-165613.4207
BOND = 4686.9923 ANGLE = 18941.9690 DIHED =
12435.7397
1-4 NB = 4282.1305 1-4 EEL = -699.7597 VDWAALS =
5129.6937
EELEC = -210390.1862 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.7925E-04
----------------------------------------------------------------------------
--
vlimit exceeded for step 71432; vmax = 20.3955
vlimit exceeded for step 71433; vmax = 99.6675
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 1095 2149 2150
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
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Received on Mon May 28 2018 - 14:00:04 PDT
