[gmx-developers] Shift for MARTINI force field?

[Luca Monticelli]

XAvier Periole wrote:
> Also for your information. The derive of temperature reported by Moritz
> et al. (linked by Michael) when using MARTINI with increasing time step
> is actually due to (the old story reported by van Gunsteren et al.) the use
> of the average of the half-time-step velocities to get the on-step
> temperature instead of the average of the half-time-step kinetic energy.
> We have written a comment on that paper ... nothing wrong with MARTINI. :))

That is also my understanding, thanks 
Xavier for clarifying this.

By the way, I think it would be useful 
if we were able to choose how to 
calculate the kinetic energy (either 
from average half-step velocities, as 
was done until v3.2.1, or from half-step 
kinetic energies, as done in v3.3 and 
newer). At the moment, one needs to use 
the (much slower) v3.2.1 to look at the 
effect of calculating the kinetic energy 
in 2 different ways. Would it be a lot 
of work to add an implementation of the 
"old way" in Gromacs 4? (and then allow 
the user to choose between the two)
I did notice large differences (in the 
density of liquids, for example) between 
v3.2.1 and v3.3 with MARTINI (with 
atomistic simulations the differences 
are less important since the time step 
is much smaller); it's clear that this 
is related to the different way of 
calculating kinetic energy, but it's not 
entirely clear to me why the new method 
would be best. I suppose Berk has done 
some work on this, but I haven't seen 
any paper published - did I miss it?

Cheers,

Luca

> 
> XAvier.
>>
>>
>>
>>
>>> Best,
>>> Michael
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