Re: [gmx-users] LINCS warnings (6153)

Hi! I had the same problem and this is what worked for me: 1. You must do an equilibration run WITHOUT any constraints (replace constrained bonds with harmonic bonds (equilibrium bond length = constraint length and force constant suitably high) and increase weight of H atoms to 10.0. 2. Do an

Re: [gmx-users] Constraints specified in .mdp as well as in .top files

? From: Mark Abraham To: Discussion list for GROMACS users 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: > Hi! > > I have a question about a possible redundancy/conflict in specifyin

[gmx-users] Constraints specified in .mdp as well as in .top files

Hi! 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 fol