[gmx-users] Re: Re: +AFs-gmx-users+AF0- twin-range cut-offs and OPLS

[Marco Möller]

Dear David,

thank You very much for Your very fast response and answer+ACE-
Might it be possible that You confused two of the parameters regarding 
the PME section? You wrote:
+AD4- rcoulomb            +AD0-  0.9
+AD4- rvdw                +AD0-  1.4
Isn' t it the other way round: 0.9 nm for rvdw, and 1.4 nm for rcoloumb?
If it isn't a typing error, where should I read to understand why in the 
PME algorithm the radius for coulomb forces can be so short, and why 
still to expect vdw-force for such a long distance?

Best regards from Germany, and THANK YOU VERY MUCH for the GROMACS 
package+ACE-

Marco.

Inst. f. Molekulare Biophysik
Johannes Gutenberg - Universitaet
55118 Mainz, Germany
moeller AT uni-mainz DOT de





----- Original Message ----- 
From: +ACI-David van der Spoel+ACI- +ADw-spoel+AEA-xray.bmc.uu.se+AD4-
To: +ACI-Discussion list for GROMACS users+ACI- +ADw-gmx-users+AEA-gromacs.org+AD4-
Sent: Thursday, March 17, 2005 11:09 AM
Subject: Re: +AFs-gmx-users+AF0- twin-range cut-offs and OPLS


On Thu, 2005-03-17 at 10:34 +010-, Marco M+AMMAtg-ller wrote:
+AD4- Dear All+ACE-
+AD4-
+AD4- I learned from the Gromacs User Guide and from some web tutorials 
+AD4- about
+AD4- MD how to use twin-range cut-offs for faster calculation of the
+AD4- non-bonded interactions. The examples were given for the GMX force
+AD4- field. As my aim is to do some first MD-runs on small peptides (13-23
+AD4- aminoacids) to learn and catch up with the method of MD without 
+AD4- wasting
+AD4- to much computer time by using mindless parameters in the mdp files: I
+AD4- appreciate any comments on the topic of choosing sensefull parameters 
+AD4- to
+AD4- bring a newbie on its MD way.
+AD4-
+AD4- My current parameters used with GMX-FF are
+AD4- in a box whith a distance of 1.0 nm between box-edges and nearest
+AD4- peptide atom:
+AD4- rlist               +AD0-  0.8
+AD4- coulombtype         +AD0-  cut-off
+AD4- rcoulomb            +AD0-  1.4
+AD4- rvdw                +AD0-  0.8
+AD4- constraints         +AD0-  all-bonds
+AD4- integrator          +AD0-  md
+AD4- dt                  +AD0-  0.002
+AD4-
+AD4- If I want to use the Gromos96/SPC and particularly the OPLSAA/TIP5P
+AD4- force-fields, can I just copy this parameters, or do I have to 
+AD4- consider
+AD4- some different boundary values? I read that it would be best to choose
+AD4- the parameters in the range of values the force-fields were optimized
+AD4- for, but up to now I did not found the information about which are the
+AD4- perfect parameters with each of the Force-fields and nothing about
+AD4- adopting them to the twin-range procedure.
For production we use something like:
rlist               +AD0-  0.9
coulombtype         +AD0-  PME
rcoulomb            +AD0-  0.9
rvdw                +AD0-  1.4
nstlist             +AD0-  5
constraints         +AD0-  all-bonds
integrator          +AD0-  md
dt                  +AD0-  0.002

If you choose not to use PME you want to change rcoulomb to 1.4 as well.
+AD4-
+AD4- Thank You very much+ACE-
+AD4- Marco Moeller
+AD4-
+AD4- ---------------
+AD4- Marco Moeller
+AD4- Inst. f. Molekulare Biophysik
+AD4- Johannes Gutenberg - Universitaet
+AD4- 55118 Mainz, Germany
+AD4-
+AD4- moeller AT uni-mainz DOT de
+AD4-
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-- 
David.
+AF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBf-
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel+AEA-xray.bmc.uu.se    spoel+AEA-gromacs.org   http://xray.bmc.uu.se/+AH4-spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++w-


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