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

From: Juraj Dobias <>
Date: Tue, 24 Nov 2020 12:35:06 +0100


I would say that your simulation is OK. Waters flying away is normal
behavior if you don't process trajectory with autoimage command in
cpptraj. And your error is also normal and you have to restart
simulation from generated restart file, or run simulation using CPU code.


On 24. 11. 20 12:09, Carlos Simmerling wrote:
> 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
> equilibration.
> Carlos
> 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 - 04:00:02 PST
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