[gmx-users] Re: abnormal flip-flop when embedding cholesterol into DOPC using CG

Xavier Periole X.Periole at rug.nl
Thu Dec 6 13:14:10 CET 2007

Dear Ran,

The reasoning of a CG-FF is a bit different than for an all-atom FF.
In a all-atom FF you assume the free energy surface the FF describes
is actually exact and the smaller the time step the more accurate
you are. You then try to increase the time step to be able to sample
bit more and increase your statistics.

In the case of a CG FF, and especially for the MARTINI one, you use
an approximated potential energy surface of the all-atom one (with a
strong smoothing of the surface) but you should reproduce all-atom and
experimental observables. Given the CG force field (set of parameters)
and thus the potential energy surface of the system, the way you
are going to explore this particular surface is actually depending
on many parameters and time step is part of them. A reduction of the
time step would favor the states of the system with the lower potential
energy. This is equivalent to play with the temperature.
This is also true for the cutoff -do not modify the cutoff- it is part
of the force field. Increasing the cutoff will not make your run more
accurate but at the contrary alter the balance of the different terms.

In summary: The time step determines the balance between enthalpy
and entropy. The smaller the time step the smaller the entropy. The
force field as been parametrized to be valid in the range 0.02/0.04 ps.

One exemple: the partitioning (used to parametrize the beads in the
MARTINI FF) is dependent on the time step. A small time step would
favor the state where the enthalpy is lower.


>> One other thing. In the CG FF the time step is considered as part of the
>> force field. Meaning that you should not play with it too much.
>> 0.04-0.02 ps is the actual range where the force field is considered
>> to reproduce experimental values of various quantities used for
>> paraameterization of the FF. Outside this range you change the balance
>> between the different terms and thus would alter the quality of the FF.
> Can you elaborate on this a bit? Surely if one changes the temperature,
> pressure, compressibility, threshold distances etc., one doesn't
> necessarily reproduces the experimental results. Too long timesteps may
> also cause a problem. But why would it be wrong to use a shorter time
> step here?
> Ran.
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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