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).
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Brett
<brettliu...@163.com>
Sent: 31 March 2016 12:22
To: gmx-us...@gromacs.org
Subject: [gmx-users] a question related to minim.mdp
Dear all,
Following is a minim.mdp from the website, in which "nsteps = 5".
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 = 5" will always work?
Brett
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 = 5 ; 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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