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

[Justin A. Lemkul]

Joanne Martin wrote:
> Hi Justin, thanks so much for the swift reply.
> With regards to the mdp setting
> 
> 
>  > The proper setting for the "dihre" keyword is either "yes" or "no."
> 
> How to I specify which dihedral I want to restrain and the force 
> constant which I want to apply to it??
> 

That's controlled in the topology.  See the manual, section 4.3.3 and table 5.6.

-Justin

> Regards,
> Joanne
> 
> On Fri, Mar 4, 2011 at 1:09 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================