[gmx-users] Langevin sd integrator: wrong average temperature

Justin Lemkul jalemkul at vt.edu
Sun May 4 15:28:38 CEST 2014

On 5/4/14, 8:36 AM, Andrey Frolov wrote:
> Dear GMX-users,
> I perform MD simulation of one point on the phase space of supercritical CO2. I use NVT ensemble with the reference T=308.15K, number molecules 548, the box size is 3.6^3 nm^3. I use different thermostats: Berendsen, v-rescale, Nose-Hoover and Langevin (sd). The problem is that "sd" integrator gives a slightly elevated temperature (by ~ 3K) compared to the reference one. Also, the potential energy is higher for simulations with "sd" integrator. This strongly depends on the integration timestep, the smaller the timestep the lower the deviation.
> I would appreciate very much if someone gives a hint why "sd" behaves unexpectedly in this case ?
> I should say that for the simulations of bulk tip3p water at ambient conditions I observe similar behavior (data not shown): the temperature tends to be slightly elevated with "sd" integrator (less than by ~ 1K, comparable to the statistical error)
> Total simulation time for each parameter set is 5 ns, the averages for the last 4 ns:
> integrator,tcoupl,tau_t[ps],dt[ps]        Average   Err.Est.  RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> md,ber,2.0,dt=0.002                          Temperature    308.2      0.0      3.4      0.0      (K)
> md,nose,2.0,dt=0.002                       Temperature    308.1      0.0      6.1      0.0      (K)
> md,vrescale,2.0,dt=0.002                 Temperature    308.1      0.1      5.9      0.6      (K)
> sd,no,2,dt=0.0005                             Temperature    308.4      0.2      6.2     -0.3      (K)
> sd,no,2,dt=0.001                               Temperature    308.8      0.1      6.2     -0.4      (K)
> sd,no,2,dt=0.002                               Temperature    311.5      0.1      6.1      0.6      (K)
> gromacs_4.6.5 (double precision).
> Also, I should note that the compressibility of the fluid is about an order higher than that of water. (~ 7.8e-4 bar^-1).
> Please, see the example "*.tpr" files in a separate e-mail.

Is the effect dependent on tau_t at all?  How did you decide on a value of 2.0? 
  Is this the correct inverse friction coefficient for supercritical CO2?  I 
have a system I'm working with (RNA in water) and with SD the temperature works 
out perfectly fine, so likely there is something specific to your system that 
needs to be considered.

Posting a full .mdp file would also be helpful.  Though you have listed most of 
the important settings, seeing everything is often useful for diagnostic purposes.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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