[gmx-users] Effect of time step size

[Justin Lemkul]

On 2/11/15 4:36 AM, Faezeh Pousaneh wrote:
> Dear Justin,
>
> Thank you.
> You are right about we must check validity of typologies attached in
> Gromacs webpage, but I just took it for test of influence of 'time step' on
> results when I was faced with similar problem in my own defined molecule. I
> initially was simulating my Lutidine molecule, so let me please give
> details of it, (running time 15 ns with same .mdp file as I sent before
> except this time both with Parrinello-Rahman, 230 molecules in rectangular
> box):
>
> dt=0.002
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Temperature                 289.953       0.03    5.63283   0.189132  (K)
> Pressure                    3.70721        2.6    389.728  -0.136095  (bar)
> Density                     956.957       0.67    8.57377    3.32218
>   (kg/m^3)
>
> dt=0.001
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Temperature                 289.994      0.033    5.70319  0.0487858  (K)
> Pressure                    1.82689        1.2    376.771    2.81752  (bar)
> Density                     967.363       0.58    8.21492    2.86186
>   (kg/m^3)
>
>
> Yes, I let time for relaxation and I ignore those times before
> equilibration. I do determine time-dependence of parameters like density
> and etc, but also I check RMSD of lutidine-lutidine in order to carefully
> collect the data which are stable. But as you see still there are
> difference in densities? Isn't is big difference?
>

Assuming the dt = 0.001 result is more accurate, it's a 1% difference, which is 
pretty consistent.  Perhaps try scaling tau-p as a function of dt so the 
coupling response is the same.  If all of the settings were the same except for 
dt, this could result in some difference.  What is the expected density with 
these force field parameters, or is it not known?

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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