Re: [AMBER] Tutorial B0

From: David A Case <>
Date: Mon, 9 Mar 2015 17:57:31 -0400

On Mon, Mar 09, 2015, Sanmeet Chahal wrote:
> I'm confused because it seems that having the epsilon as 0.0 was what was
> causing the segfault when I ran the run minimization step of Tutorial B0
> because after changing the epsilon to be a non-zero value the error stopped
> occurring. Could some one please explain when it is ok to set LJ parameters
> to 0 and when they could cause an error?

General rule is that zero vdW parameters will only work for atoms (hydrogens
or dummy atoms, usually) whose bond lengths to a neighboring atom are fixed
by SHAKE or SETTLE. I'm not sure what value of ntc you were using in your
minimization steps.

[Many investigators have decried the very early decision to have zero vdW
parameters in force fields: they cause all kinds of problems. Be sure you
really need to do this if you are creating your own.]

You may occasionally get away with violating this rule. Also, segfaults might
be from something else (i.e. an indirect consequence of having zero vdW
parameters, that in turn lead to some other unexpected behavior.)


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Received on Mon Mar 09 2015 - 15:00:03 PDT
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