[gmx-users] Constraints specified in .mdp as well as in .top files
vishwanathhdalvi at yahoo.co.in
Fri May 15 20:46:15 CEST 2009
Thank you for your response. I am still unclear as to how the whole thing works (and the manual is no help).
If I do specify (in the .mdp file) something like constraints = all-bonds, will that override the harmonic-bond interactions specified in the .itp files?
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, 14 May, 2009 4:56:04 PM
Subject: Re: [gmx-users] Constraints specified in .mdp as well as in .top files
Vishwanath Dalvi wrote:
> I have a question about a possible redundancy/conflict in specifying bond-constraints.
> I have in my simulation (among other things) a number of bonds - some of which are harmonic while some are rigid (or constrained).
> I specify the bonds in the .itp (or ultimately in the .top) files as follows:
> [ bonds ]
> ; index1 index2 func deq(nm) k(kJ/mol/nm2)
> 1 2 1 0.1529000000 224262.4000000000
> 1 32 1 0.1810000000 185769.6000000000
> 2 3 1 0.1529000000 224262.4000000000
> 3 4 1 0.1529000000 224262.4000000000
> [ constraints ]
> ; index1 index2 funct length(nm)
> 1 30 1 0.1090000000
> 1 31 1 0.1090000000
> 2 28 1 0.1090000000
> 2 29 1 0.1090000000
> However, it turns out that the .mdp file also requires one to specify constraints in the form of:
> constraints = all-bonds/h-bonds etc
> Do we have to specify constraints in the .mdp file if we already have specified them in the .itp file?
I believe so. This is also true of restraints (which are a different concept in GROMACS).
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