Hi, 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" http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2004/exercises/index_html https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html 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
prodVacuum.mdp
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