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

Andreas Boozo Frank andreas.frank at ch.tum.de
Wed Mar 12 17:20:19 CET 2008

Dear all,

I think I found the reason for the deviation after "hunderds of small 
runs"...:-): I normally used Dispersion Correction for both the energy 
and pressure because in the manual the following is noted:

"...The pressure correction in contrast is very large and can not be 
neglected. Although it is in principle possible to
parameterize a force field such that the pressure is close to 1 bar even 
without correction, such a method makes
the parameterization dependent on the cut-off and is therefore 
undesirable. Please note that it is not consistent to
use the long range correction to the dispersion without using either a 
reaction field method or a proper long range
electrostatics method such as Ewald summation or PPPM."

Maybe I got it wrong (and I am still a little bit confused) but because 
I used the reaction-field approximation I turned on DispCorr for 
Pressure. However, it seems that the Gromos DMSO FF was established in a 
way that the correction is "included" in the parameter set which was / 
is not clear to me when reading the DMSO paper.

And thank you Berk for the explanation of the Orire parameters.



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.
> ------------------------------------------------------------------------
> Express yourself instantly with MSN Messenger! MSN Messenger 
> <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
>gmx-users mailing list    gmx-users at gromacs.org
>Please search the archive at http://www.gromacs.org/search before posting!
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php


More information about the gromacs.org_gmx-users mailing list