[gmx-users] a question related to minim.mdp

Christopher Neale chris.neale at alum.utoronto.ca
Thu Mar 31 18:53:32 CEST 2016

It depends on what you want to do. If you simply want to minimize the system so that the dynamics will be stable in MD, then I have never needed more than 500 steps of minimization (though in some cases I find it necessary to use flexible waters and solutes via the mdp options define=-DFLEXIBLE and constraints=none). On the other hand, if you're trying to find a minimized structure for normal mode analysis, I gather from previous posts that one has to get really right to the potential energy minimum, which would mean setting nsteps arbitrarily large and letting the program define when no more minimization can be accomplished (perhaps among other things like the right combination of minimization schemes).


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Brett <brettliu123 at 163.com>
Sent: 31 March 2016 12:22
To: gmx-users at gromacs.org
Subject: [gmx-users] a question related to minim.mdp

Dear all,

Following is a minim.mdp from the website, in which "nsteps      = 50000".

Here what I want to ask is, does it mean the larger the protein, the larger the value of nsteps? Or for any size of protein regardless of mw, as for it has specified "emtol       = 500.0",  " nsteps      = 50000" will always work?


minim.mdp was as following,

"; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep     ; Algorithm (steep = steepest descent minimization)
emtol       = 500.0    ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps      = 50000     ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist     = 1         ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type     = grid      ; Method to determine neighbor list (simple, grid)
coulombtype = PME       ; Treatment of long range electrostatic interactions
rcoulomb    = 1.4       ; Short-range electrostatic cut-off
rvdw        = 1.4       ; Short-range Van der Waals cut-off
pbc         = xyz       ; Periodic Boundary Conditions"
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