From: "chetana baliga" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
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
results.
Berk.
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