[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

James Starlight jmsstarlight at gmail.com
Sun Feb 5 15:40:24 CET 2012


Larger cutoffs would not only make the problem worse (read the error
> message carefully and consider the minimum image convention), but it would
> also potentially break the validity of the force field model.  The vdW
> cutoff for Gromos96 should be 1.4 nm, not 0.9 nm, in any case.

This sounds controversially alitle :)

Today I've tried such simulation with the 1.2 cutoffs and obtain the same
error on the 3rd ns ( density was 1.35 )
>From the error message I've understood that the problem was due to the Z-
box vector wich was decreased up to the 3 nm ( this is smaller rhan 2x 1.2
of R_list cutoff ). So in accordance to that message I understood that
cutof must be > 1.5 in the case of my system didnt it?

By the way  I never seen such large cutoff distance in the Gromos
parameters. IS there any else way to solve my problem ?

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