[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

[Justin A. Lemkul]

Joanne Martin wrote:
> Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs 
> version 4.04.
> 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 error >
> 
> 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'
> 

The proper setting for the "dihre" keyword is either "yes" or "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 
> restraints.
> 
> 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?
> 

You need to generate any intermediate structures at angles you wish to sample. 
There is no mechanism to enforce the rotation about a dihedral presently 
implemented in Gromacs.

> 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??)

The pull code is irrelevant here.  Please do not attempt to apply my tutorial to 
your problem (beyond basic theory), as you will probably only frustrate yourself 
by doing so.

When using a dihedral restraint, an energy term corresponding to the restraint 
should be written to the .edr file.  I imagine you can plot these values as a 
function of the dihedral angle to extract the information you want.

-Justin

> 
> ; 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,
> 
> 
> Kindest regards,
> Joanne
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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