Re: [gmx-users] Constraints Restraints

2009-11-12 Thread Ran Friedman
+0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Constraints Restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 8ff89815091245u63c6aa65sa839f24634352...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell

[gmx-users] Constraints Restraints

2009-11-12 Thread Darrell Koskinen
. Darrell Date: Thu, 12 Nov 2009 14:16:06 +0100 From: Ran Friedman r.fried...@bioc.uzh.ch Subject: Re: [gmx-users] Constraints Restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4afc0a96@bioc.uzh.ch Content-Type: text/plain; charset=ISO-8859-1 Erik Marklund wrote

Re: [gmx-users] Constraints Restraints

2009-11-12 Thread Justin A. Lemkul
Darrell Koskinen wrote: Thanks for the additional comments. So given that, in my system, I have H atoms attached to C atoms on the perimeter of a finite graphene sheet that is placed above multiple infinite layers of graphene (graphite), would it be more appropriate to use: (i) a classical

[gmx-users] Constraints Restraints

2009-11-11 Thread darrellk
Hi, I just have a quick question on contraints and restraints. My understanding is that constraints fix the position of an atom in space and restraints restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a little confused by the purpose of

Re: [gmx-users] Constraints Restraints

2009-11-11 Thread Justin A. Lemkul
darre...@ece.ubc.ca wrote: Hi, I just have a quick question on contraints and restraints. My understanding is that constraints fix the position of an atom in space and restraints restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a

Re: [gmx-users] Constraints Restraints

2009-11-11 Thread Tsjerk Wassenaar
Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like

[gmx-users] Constraints Restraints

2009-11-11 Thread Darrell Koskinen
Date: Wed, 11 Nov 2009 21:45:44 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Constraints Restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 8ff89815091245u63c6aa65sa839f24634352...@mail.gmail.com Content-Type: text/plain; charset

Re: [gmx-users] Constraints Restraints

2009-11-11 Thread Mark Abraham
in GROMACS manual). Mark Date: Wed, 11 Nov 2009 21:45:44 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Constraints Restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 8ff89815091245u63c6aa65sa839f24634352...@mail.gmail.com Content