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

[Johnny Lu]

The jump is much smaller though, and seems to decrease as I do more
continuation.

These tripeptide simulations all use the same mdp file, without the shift
potential, and with those ultra-conservative settings.

http://oi57.tinypic.com/15f2mx1.jpg

The order of restarts:
Black -> Red -> Green -> Blue.

Here is the example command I used to continue the simulation.

grompp_d  -f md_0_10.mdp -c md_0_9.tpr -t md_0_9.cpt -p topol.top -o
md_0_10.tpr

On Wed, Nov 12, 2014 at 10:16 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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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>>
>>
>