[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04
Justin A. Lemkul
jalemkul at vt.edu
Fri Mar 4 18:05:53 CET 2011
Joanne Martin wrote:
> Thanks Justin,
> I think I have the restraints section sorted...........
>
> However, once all of the dihedrals are obtained from the MDs, I would
> like to do a WHAM analysis, of the reaction pathway.
> As I have to run each conformation as a separate MD in order to obtain
> all dihedral conformations, how can I do this.
Do what? Sorry, I'm not clear on what you mean here. You need a series of
starting configurations that you use to run independent MD simulations. How you
generate those configurations is up to you, either manually editing the
structure, running unrestrained MD and dumping out frames corresponding to the
desired angles, etc.
> g-wham in gmx requires .pdo files from the US output, but since I cannot
.pdo files have not been required since Gromacs 3.3.3. The new format is simple
.xvg files.
> use US (in the classical sense) for a dihedral, how can i generate a
> final plot of free energy vrs dihedral???
I don't know if g_wham is going to be useful here, since you're not using the
pull code and hence your runs won't generate pullf/x.xvg files, which are what
g_wham reads. You may want to look into the literature for how people calculate
this.
-Justin
> Thanks again, for all the help,
> Joanne
>
>
>
> On Fri,. Mar 4, 2011 at 1:33 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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> <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 <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
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