[AMBER] AMBER NFE SMD calculation with new collective variable

From: <georg.kuenze.vanderbilt.edu>
Date: Mon, 28 May 2018 16:51:41 -0400

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
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