[gmx-users] Vacuum Simulation of Alanine Dipeptide =>production run

M. Emal Alekozai memala at gmx.net
Fri Aug 22 06:59:22 CEST 2008


to create some toy data I want to do a vacuum simulation of Alanine Dipeptide with Gromacs.
For the production run script I used the gmx-user mailing list thread [1a-d], the tutorial [2] and the corresponding sample script [3].

1a: http://www.gromacs.org/pipermail/gmx-users/2006-August/023245.html
1b: http://www.gromacs.org/pipermail/gmx-users/2006-August/023248.html
1c: http://www.gromacs.org/pipermail/gmx-users/2006-August/023250.html
1d: http://www.gromacs.org/pipermail/gmx-users/2006-August/023249.html
2: "Gromacs course in 2004 -> Gromacs exercises"
3: https://extras.csc.fi/chem/courses/gmx2004/exercises/exercise.tgz

I got three questions about my production run setup:

1. comm_mode
In [1c] David van der Spoel suggests to use "comm_mode=Angular" (... remove angular center of mass motion ...).
A few seconds later in [1d] Gerrit Gronhof suggests to use "comm_mode=linear"
(... In addition to Erik and my suggestions, you should also remove the 
overall rotation: comm_mode=linear. ...)
I'm know a little confused, I checked the Gromacs manual and it says if I use "comm_mode=Angular" the center of mass translation and rotation around the center of mass is removed.
Do I rally need to use  something like "comm_mode=Angular, linear" ???

2. comm_grps
If I use "comm_grps="  is the default value (all atoms of system) used?

3. I changed some settings in David van der Spoel's Vacuum production run script [3]. The modified script is attached. The main changes are:
	;dt= 0.004 ; MEA
	dt= 0.002 ; MEA
	;epsilon-r= 1 ; MEA
	epsilon-r= 80 ; MEA
Are they reasonable with the other options in the script (or do I have to adjust also other values)?

Thanks Emal

Psssst! Schon das coole Video vom GMX MultiMessenger gesehen?
Der Eine für Alle: http://www.gmx.net/de/go/messenger03
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