[gmx-users] Can we compare results from versions 3.2 & 3.3.1

Berk Hess gmx3 at hotmail.com
Wed Feb 14 14:16:37 CET 2007

>From: "chetana baliga" <baliga.chetana at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Can we compare results from versions 3.2 & 3.3.1
>Date: Wed, 14 Feb 2007 18:28:16 +0530
>Dear Users,
>I have simulation data collected using Gromacs version 3.2 . As it was
>allowed in that version, I have used r_list = 1.1, r_coulomb = 1.0,
>r_vdw = 1.0, with PME coulomb type and switch for vdw type , while
>collecting the data.
>Now, I am running another simulation using the recent 3.3.1 version.
>Here , it is mandatory to use r_list = r_coulomb, but r_list should be
>0.1 to 0.3 greater than r_vdw for switch vdw type. So, I have set my
>parameters to be r_list = r_coulomb = 1.1, while I have retained r_vdw
>at 1.0 . I want to know if the data collected by these two methods can
>be compared?? Would the change in r_couomb have a pronounced effect on
>the system?

In mdrun 3.2 the coulomb cut-off is actually equal to rlist for your setup
(that is why I added a check for this in grompp of 3.3.1).
So the only difference between the two setups is that your ewald beta
parameter will be slightly different, as it is determined by grompp using
rcoulomb and ewald_rtol. This will probably have little influence on the 


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