[gmx-users] Re: Improving Energy Conservation in NVE Simulation of Water

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 28 18:51:26 CEST 2011

Andrew DeYoung wrote:
> Hi, 
> Thank you.  I tried again, this time doing 100 ps of NVT equlibration,
> followed by 500 ps of NVE.  I have posted my results here:
> http://www.andrew.cmu.edu/user/adeyoung/july27/withnvt.pdf
> But, they are not much better.  For the NVT equilibration, I used v-rescale
> temperature coupling with tau_t = 2 ps.  What kind of temperature coupling
> do you typically use or recommend?

That sounds reasonable, although a 2-ps coupling time is a bit long for 
V-rescale.  Your results indicate that the system still is not stable, even in 
NVT.  Temperature should not fluctuate very much after the first few ps.  Try a 
longer NVT.

What motivated your choice of cutoffs?  They seem arbitrary and too long.  You 
may be seeing effects of the classic "flying ice cube" problem where isolated 
elements of the system start to (essentially) freeze.


> Thanks,
> Andrew
> Andrew DeYoung wrote:
>> Hi, 
>> I have been simulating 1000 SPC/E water molecules in the NVE ensemble (by
>> using tcoupl = no and pcoupl = no).  In these simulations, I am
> considering
>> only Lennard-Jones interactions; I have "turned charges off" by setting
> the
>> partial charges on oxygen and hydrogen to zero in a local copy of spce.itp
>> that I include in my topology file.  
>> If you have time, I have posted a pdf file containing a summary of what I
>> have tried so far:
> http://www.andrew.cmu.edu/user/adeyoung/july27/july27.pdf
>> At first, I tried using vdwtype = Cut-off.  However, Gromacs gave me a
> note
>> message: 
>> ---
>> NOTE:
>> You are using a cut-off for VdW interactions with NVE, for good energy
>> conservation use vdwtype = Shift (possibly with DispCorr)
>> ---
>> I ignored this note message and ran the simulation anyway.  Indeed, as
>> Gromacs warned me, the (total) energy conservation is very bad; the total
>> energy decreases seemingly significantly in what appears to be an almost
>> linear fashion.  I have done energy minimization, equilibration, and
>> production dynamics, but for simplicity, I have drawn the equilibration
> and
>> production dynamics results in the same color in the pdf file that I have
>> posted.  
>> (As far as energy minimization, I did a series of two energy minimization
>> steps.  First, I used integrator = l-bfgs with dt = 0.001 ps, nsteps =
>> 10000, emstep = 0.01 nm, and emtol = 10.0 kJ mol^-1 nm^-1.  I got the
>> following results:
>> Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
>> Potential Energy  = -9.3022546e+02
>> Maximum force     =  5.5933684e-01 on atom 1123
>> Norm of force     =  1.9135195e-01
>> So, it seems that the energy of the configuration is quite low--the water
>> molecules are relatively far apart from one another (the simulation box is
>> quite large).  
>> Next, I used integrator = steep (passing the ending configuration from the
>> l-bfgs minimization to grompp using -t followed by the trajectory file)
> with
>> dt = 0.001 ps, nsteps = 10000, emstep = 0.01 nm, and emtol = 10.0 kJ
> mol^-1
>> nm^-1.  I got the following results:
>> Steepest Descents converged to Fmax < 10 in 1 steps
>> Potential Energy  = -1.2968502e+03
>> Maximum force     =  7.0817396e-02 on atom 820
>> Norm of force     =  2.6016856e-02
>> This configuration seems probably acceptable.  So much for energy
>> minimization.)
>> Secondly, I used vdwtype = Shift as the note message recommended.  I tried
>> two different sets of values of rlist, rvdw_switch, rvdw, and rcoulomb.
>> But, in both cases, energy conservation is bad--almost as bad as when I
> used
>> vdwtype = Cut-off.  
>> If you have time, can you please look at the pdf file that I have posted
>> (http://www.andrew.cmu.edu/user/adeyoung/july27/july27.pdf)?  Do you have
>> any suggestions of other vdw types or vdw parameters that I should try to
>> hopefully improve energy conservation?  On page 1, I have displayed the
>> total energy results.  On pages 2 and 3, I have pasted a typical .mdp file
>> that I used and also the results of other quantities from the simulations.
>> One thing that I notice is, on the bottom of page 2, it appears that the
>> _potential_ energy conservation is good, whereas the kinetic energy
>> conservation is quite bad.  Do you know, what sort of clue should this
> fact
>> give me as to what is going on with my system?  
> What seems most obvious to me is that your system is cooling down because
> your 
> molecules are slowing down.  Your gen_temp is set to 298 K, but your initial
> velocity distribution produces a temperature over 305 K, so you're not
> exploring 
> the energy surface you think you are.  Certainly in NVE temperature is not 
> necessarily a conserved quantity (the total energy is), but you're not
> starting 
> under the conditions you want.  The temperature in all of these cases is
> only 
> approaching the desired 298 K towards the end of the 500 ps timeframe you've
> shown.  Try an NVT equilibration at 298 K first, then switch to NVE.
> The other thing to consider is whether or not this should even work.  You've
> taken a condensed-phase water model that is largely held together by
> hydrogen 
> bonding and transformed it into a semi-gas state and removed the most potent
> interactions that keep the molecules together.  Force fields must balance LJ
> and 
> electrostatic terms to reproduce some desired behavior.  In this case,
> you're 
> eliminating half of the equation (or more, depending on how the LJ and 
> electrostatic terms are balanced to contribute to stability).
> I would suggest that if you have to hack this model under these conditions, 
> start with NVT equilibration before moving to NVE.  Even better would be to
> use 
> a simpler system, like an ideal gas that only has LJ terms, and determine
> the 
> proper protocol for obtaining a stable NVE ensemble.  That way, you're not 
> stabbing in the dark as to what the appropriate settings should be in the
> .mdp file.
> -Justin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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