PS: to increase skinnb value, add
&ewald
skinnb=5,
/
to the input file.
Regards!
El lun., 22 jun. 2020 08:39, Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
escribió:
> Hi there!
> How long is your heating step? Because if its too long you will have to
> restart the calculation every 500ps (roughly) and increase the skinnb
> value, due to changes in system density during the heating. Pmemd.cuda does
> not recalculate the non bond list cells, so if they change too much due to
> changes in system size, program will stop.
> Hope it helps!
> Gera!
>
> El lun., 22 jun. 2020 08:22, <rosaester.forgione.unina.it> escribió:
>
>> I want to add that after some steps of the production the same error
>> appears 2/3 times and then the calculation stops :
>>
>> PRODUCTION
>> Mon 22 Jun 2020 01:12:04 PM WEST 1 ns
>> Mon 22 Jun 2020 01:15:26 PM WEST 2 ns
>> Mon 22 Jun 2020 01:18:49 PM WEST 3 ns
>> 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.
>>
>> Mon 22 Jun 2020 01:19:58 PM WEST 4 ns
>> 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.
>>
>> Mon 22 Jun 2020 01:20:00 PM WEST 5 ns
>>
>> Unit 9 Error on OPEN: PRODUCTION-4.restrt
>> STOP PMEMD Terminated Abnormally!
>>
>>
>>
>> Quoting rosaester.forgione.unina.it:
>>
>> > Hi,
>> >
>> > I am facing problems in running MD dynamics by using PMEMD.CUDA
>> >
>> > During the 300 K heating step (NPT) the following error appears:
>> >
>> > 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.
>> >
>> > However, the MD simulations goes on passing to the production steps.
>> >
>> > I tried to restart the simulation from the previous restart file, as
>> > suggested by the error message, but it doesn't work since the same
>> > error appears.
>> >
>> > I used the same equilibration protocol that I routinely use to
>> > carry on MDs on ligands alone (glycans) and protein-ligand complex.
>> >
>> > I tried to run a MD simulation on an "old" system, already analyzed
>> > with amber without any issue, and the same error appears. Thus, it
>> > seems that the problem is not strictly related to the parameters of
>> > the system.
>> > I also run the simulation on GPU 0 and then on 1 and the error is
>> > still there.
>> >
>> > Anyone can suggest how to fix this problem?
>> >
>> > Thanks in advance,
>> >
>> > Rosa
>> >
>> >
>>
>>
>>
>>
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>
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Received on Mon Jun 22 2020 - 05:00:03 PDT
