Generic debug for learning to handle blowups:
1. Plot out energies and volume. Energy components are of interest.
2. View trajectory.
3. Rerun with saving mdout, mdcrd more frequently if needed to get
better data.
4. Often there will be a cryptic message in mdout about two atoms, with
atom numbers, right as things go off the rails. Typically the force
field(s) for those atoms have some weakness that allows them to
superimpose, with two mos common causes (in order): one or both atoms'
vdw was mal-designed by you; or it involves highly-negative O's e.g. in
phosphates bending into some atom that, for it, is way too positive for
the Christmas season. :-)
Caveat/plus: these steps date back to the 1990's.
Bill
On 12/17/18 11:25 PM, Gustaf Olsson wrote:
> I don’t know what you are running, of course, though from previous experience with similar issues I have two suggestions
>
> Try to reconstruct the system, if possible, and make sure that you don’t have to much dead-space nor to little since both of these things can be issues while equilibrating
>
> Check the parameters of your structures, due to a parameterisation issue a few years ago I had a structure “chasing its own tail”, accelerating until the simulation halted.
>
> Best regards
> // Gustaf
>
>
>> On 18 Dec 2018, at 07:01, Nisha Amarnath Jonniya <phd1601271002.iiti.ac.in> wrote:
>>
>> Dear AMber user,
>>
>>
>> I would like to run amd for my system containing protein, ligand, ANP and
>> MN. But while running get the following error.
>>
>> ####################################################
>> 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.
>> #####################################################
>> Even I tried the last alternative by slowing heating in steps and
>> removing the restraint slowing and till the density convergence in CPU ,
>> then run its equilibration in GPU.
>>
>> Please suggest.
>>
>> --
>>
>> Nisha Amarnath Jonniya
>> PhD Research Scholar
>> Biosciences and Biomedical Engineering
>> Indian Institute of Technology, Indore
>> India
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>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Dec 18 2018 - 00:00:01 PST
