[gmx-users] Re: DMSO G53a6 FF in Gromacs
gmx3 at hotmail.com
Wed Mar 12 15:31:10 CET 2008
> Date: Wed, 12 Mar 2008 12:31:12 +0100
> From: andreas.frank at ch.tum.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: DMSO G53a6 FF in Gromacs
> Hi Berk,
> Thanks for replying so quick. I made it rigid in that way that I used
> bonded interactions also for the groups that are not directly connected
> (FF parameters gb_49 & gb_50) and then applied all-bond SHAKE. For the
> other bonds I used gb_41, gb42 and for the three angles ga_45 and ga_46.
There could be another issue.
With reaction-field you always introduce integration errors.
With water this leads to a temperature of 305 K when Berendsen coupling
to 300 K with tau_t=0.1 ps and the Gromos cut-off setup.
In Gromos there is/was a problem with inconsistent ways of determining
the temperature. Therefore the effective temperature in the simulation
can be several degrees higher than the one reported in the paper.
What coupling method did you use and what is your real temperature?
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