[gmx-users] restarting of shifted potential, 4.6.7 bug?

[Johnny Lu]

This seems to have nothing to do with shifted potentials or gpu.

I run a tripeptide double precisiion NVE simulation on a machine with xeon
cpu and without gpu. kill it, then continue it with the cpt file generated.
That energy jump still exists.

On Tue, Nov 11, 2014 at 1:39 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Going from non-shift to shifted potential changes the energy. So I was not
> surprised by the sudden jump of energy between step 0 and step 10 for the
> previous simulation (npt14).
>
> But the jump near step 0 for the current simulation (npt15) is not right.
>
> This is an equilibration run.
>
> I have just uploaded the files at http://redmine.gromacs.org/issues/1640
>
>
> On Tue, Nov 11, 2014 at 10:54 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu <johnny.lu128 at gmail.com>
>> wrote:
>>
>> > Hi.
>> >
>> > I ran 30ns NPT with Potential-shift-Verlet on both potentials,
>> continuing
>> > from a NPT without Potential-shift-Verlet. The energy dropped from -3e5
>> to
>> > -4e5, which is fine.
>> >
>> > After that, I continue the 30ns NPT with the same mdp file, except with
>> a
>> > longer run time (300ns).
>> >
>> > The total energy was -4e5 at step 0, and then -3e5 at step 5000, and
>> now at
>> > about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed
>> after
>> > step 0?
>> >
>>
>> IIRC, the restart ought to compute the same energy on the initial
>> coordinates as it did at the end of the previous run, and even if there's
>> no re-computation on the same coordinates, obviously it should not  jump
>> by
>> 1e5 in a few steps (or one? can't tell from the resolution). I would think
>> that might be a bug in filling a data structure for the output, but
>> probably not one in the simulation itself. Please file an issue at
>> http://redmine.gromacs.org, tarballing all the relevant files, and I'll
>> try
>> to look at it.
>>
>> The long-time behaviour of both simulations is pretty suspect though.
>> Since
>> you're prepared to be ultra-conservative with your non-bonded and SETTLE
>> settings, I would explore using a 0.5fs time step (in normal and
>> ultra-conservative mode). Berendsen is not a good barostat algorithm for
>> production work, too... but I would not expect such a problem from its
>> use.
>> Perhaps more importantly, why are you turning off the long-range
>> dispersion
>> correction?
>>
>> Mark
>>
>> I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
>> > grompp for both simulations.
>> >
>> > The plot of total energies for the two simulations:
>> > http://oi60.tinypic.com/ddmejd.jpg
>> > The two mdp files: http://oi58.tinypic.com/11980si.jpg
>> >
>> > The commands that I used for continuing the simulations:
>> >
>> > The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp
>> -f
>> > npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr
>> >
>> > The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp
>> -f
>> > npt15.mdp -c npt14.tpr -t npt14_step30000000.cpt -o npt15.tpr
>> >
>> > Thanks.
>> > --
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