Re: [AMBER] NVT equilibration crash using CUDA

From: James Starlight <>
Date: Mon, 9 Jun 2014 12:34:29 +0400

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


2014-06-09 12:17 GMT+04:00 James Starlight <>:

> 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
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