Hi, Georg
It looks like your SMD simulation has conflicts with the SHAKE, and leads
to the vlimit error. Possible reason is that you used a too large steering
strength
or too short time. I would recommend you to lower the steering strength and
increase
the steering time. If this still happens, it is mostly likely that your new
CV has some
problems. You can check your md trajectories to see which part of your
structure
started to blow up and how is it related with your steering of new CV.
Best
Feng
On Mon, May 28, 2018 at 4:51 PM, <georg.kuenze.vanderbilt.edu> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Wed May 30 2018 - 11:30:03 PDT
