[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04
joanne.c.martin at hotmail.com
Fri Mar 4 14:02:51 CET 2011
Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs version
I have read through all posts on the mailing list regarding this query, and
although Chris Neale did explain how to set the restraints for Gromacs 3,
these options are now obsolete for 4.04............ I get the following
Ignoring obsolete mdp entry 'domain-decomposition'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Ignoring obsolete mdp entry 'dihre_tau'
Ignoring obsolete mdp entry 'nstdihreout'
Ignoring obsolete mdp entry 'nstcheckpoint'
ERROR: invalid enum 'simple' for variable dihre, using 'no'
I have read Chris's paper from 2008 on alanine dihedrals but again this is
done using Gromacs 3, and his tutorial for US in based on distance
Basically I have two conformations of a sugar ( a starting conformation and
an end conformation), and I want to generate a series of snapshots ie a
reaction coordinate, from a "pulled" MD, for use in US.
The pull code is only applicable to distance restraints, so how can I apply
a restraint to the dihedral so that it will sample all dihedrals from the
initial -180deg through to the end +180deg?
I would really appreciate if someone could explain to me, where I should set
the restraints, as this is not clear from the manual.
Also once the initial configurations are generated, is the below mdp option
accurate for US of a dihedral >
(query regarding distance option should this be direction??)
; Pull code
pull = umbrella
pull_geometry = *distance* ; can't get PMF with direction
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = ?
pull_group1 = ?
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
Can someone please get back to me with any suggestions you may have,
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