[gmx-users] Re: DMSO G53a6 FF in Gromacs

Andreas Boozo Frank andreas.frank at ch.tum.de
Wed Mar 12 15:46:43 CET 2008

Hi Berk,

I used weak berendsen temperature coupling with tau_t = 0.1 and a ref_t 
of 298.15 K. My average temperature during the NPT run (disregarding the 
first 100 ps) is ca. 298.20 K (as given by g_energy).
I had another question to you, Berk, in my last mail to the list maybe 
two hours ago, regarding your Orientation Restraints algorithm. Have you 
seen this or should I repost it?

Best regards,


Berk Hess wrote:

> ------------------------------------------------------------------------
> > 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.
> >
> > Andreas
> 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?
> Berk.
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