I don't see any obvious problem in the input (others might), but here are a
few suggestions:
- this isn't really a "heating" step, since you assign the thermostat to
300K immediately. It will be a very fast heating from 0K to 300K, and in my
experience that can cause problems. Heat more slowly, or assign the initial
velocities (tempi) to something more than 0K.
- have you tried without respa? especially during equilibration...
- look at the atoms indicated in the shake failure. Anything unusual
about the structure, or about those atoms? We don't know what you are
simulating and if there are any unusual force field changes included, and
so on. For example, this could be a symptom of a problem with force field
modifications, if you made any.
On Thu, Oct 26, 2017 at 8:01 AM, Jeyaram R A <ra.jeyaram.vit.ac.in> wrote:
> Dear Amber Users,
>
>
>
> During the equilibration step, the PMEMD stop
> Abnormally. The output file shows as "Coordinate resetting cannot be
> accomplished,
> deviation is too large". How to solve this problem?, Here i attach
> the equilibration.in and eq.out files
>
>
> with regards,
>
> R. A. Jeyaram
>
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>
>
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Received on Thu Oct 26 2017 - 05:30:02 PDT
