[gmx-users] Energy Drift

Per Larsson per.larsson at sbc.su.se
Wed Oct 19 08:46:43 CEST 2011

Hi Justin!

Do you maybe have an example of such a protein (preferably not too large :-), that I could run some tests on?

I'd be interested in seeing if there has been any bugs introduced in the cutoff code that destabilises proteins that way.


18 okt 2011 kl. 23:41 skrev "Justin A. Lemkul" <jalemkul at vt.edu>:

> Ben Reynwar wrote:
>> I posted to the list a few days ago with an energy drift problem.
>> Mark Abraham helpfully suggested using all-bonds rather than h-bonds
>> which solved the problem.  I'm now trying to understand quite why that
>> helped so much.
>> The simulation is a protein of about 5000 atoms using GBSA, a time
>> step of 2 fs, and a cut-off of 1.6 for VdW, coulomb and GB.
>> I've run energy drift simulations using the md integrator, with no
>> thermostat, and using the ld integrator with a tau_t of 1000000.
>> Simulations were run changing various parameters.  The changes were:
>> - dt reduced to 1.5
>> - dt reduced to 1.0
>> - cutoff increased to 2.0
>> - constraint changed from h-bonds to all-bonds
>> Plot of the energy drifts can be seen at
>> http://www.reynwar.net/ben/gromacs/energy_drift.png.
>> Noticeable features are:
>> - changing the time step makes no difference (in my last post I
>> claimed it did, which is why you should make plots rather than
>> eyeballing log files).
>> - increasing the cut-off helps a lot.
>> - changing constraint to all-bonds make a dramatic difference
>> - using ld there is a downwards drift in the energy when using
>> all-bonds constraint.  The temperature is roughly 300 K and the set
>> point is 400 K so this downwards drift seems unlikely to be due to
>> coupling to the langevin thermostat.
>> My questions are:
>> - why does the all-bonds constraint help so much?
>> - why doesn't moving to a smaller time step help with this?
>> - what is the cause of the downwards drift when using ld with all-bonds?
> I can offer a bit of general advice here, but no specific answers.  Hopefully it helps.  To get at the root cause of all of this, you should be analyzing individual energy components, not just the total energy.  These will tell you which terms are systematically changing.
> In my experience with GB simulations, using anything other than infinite cutoffs (i.e. all-vs-all kernel) has resulted in unstable simulations.  I don't mean that the simulations crash or anything, but the results are clearly incorrect. Stably folded proteins have drastically increased RMSD and lose their structure very easily.  The effect is independent of the chosen force field.  I would recommend always using infinite cutoffs for GB simulations.  It may improve your situation.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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