also please suggest me where in input file I should provide exactly box
type used for the simulation. I had the problems with the rectangular boxes
(not with the cubic) in spite of usage of ntp=3 with constant surface
tension.
James
2014-06-09 12:17 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> Dear Amber users!
>
>
> I've faced with the problems during equilibration of my protein using
> pmemd.cuda
>
> 1- I've started to heat my protein in nvt and quickly obtained
>
> ERROR: Calculation halted. Periodic box dimensions have changed too much
> from their initial values.
> Your system density has likely changed by a large amount, probably from
> starting the simulation from a structure a long way from equilibrium.
>
> [Although this error can also occur if the simulation has blown up for
> some reason]
>
> The GPU code does not automatically reorganize grid cells and thus you
> will need to restart the calculation from the previous restart file.
> This will generate new grid cells and allow the calculation to continue.
> It may be necessary to repeat this restarting multiple times if your
> system
> is a long way from an equilibrated density.
>
> Alternatively you can run with the CPU code until the density has
> converged
> and then switch back to the GPU code.
>
> visualization show me that individual water have been moved towards the
> box boundaries being separated from the rest of the solvent.
>
> What would be best solution here
>
> 1- Switch to the sander and perform all equilibration using cpu
>
> 2- Do equilibration using cuda starting in NPT (with frozen protein) with
> applied barostat preventing such density artifacts ?
>
> James
>
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Received on Mon Jun 09 2014 - 02:00:03 PDT
