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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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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