Re: [AMBER] System blows up when simulating under npt

From: Carlos Simmerling <>
Date: Tue, 24 Nov 2020 06:09:42 -0500

Have you tried the simulation without adding the adduct? Also you didn't
describe your equilibration protocol. I believe the one we used should be
described in our paper on that system. Dan Roe also has a nice paper on

On Tue, Nov 24, 2020, 6:05 AM Amit Sharma (Asstt. Prof., MCARS) <> wrote:

> Hi,
> I trying to simulate protein having of FMN Cys adduct.
> When running md using nvt and positional restraints of 0.5 kcal mol-1 A-2
> on the protein, the system remains fine.
> But as I switch to npt and remove all the restraints system blows up and
> water molecules start flying away.
> Error message is as follows:
> "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."
> Can anyone suggest how to deal with this?
> Thank You,
> Amit
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Received on Tue Nov 24 2020 - 03:30:02 PST
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