Thanks Justin,<br>I think I have the restraints section sorted...........<br><br>However, once all of the dihedrals are obtained from the MDs, I would like to do a WHAM analysis, of the reaction pathway. <br>As I have to run each conformation as a separate MD in order to obtain all dihedral conformations, how can I do this. <br>
g-wham in gmx requires .pdo files from the US output, but since I cannot use US (in the classical sense) for a dihedral, how can i generate a final plot of free energy vrs dihedral???<br>Thanks again, for all the help,<br>
Joanne<br><br><br><br><div class="gmail_quote">On Fri,. Mar 4, 2011 at 1:33 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><br>
<br>
Joanne Martin wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Justin, thanks so much for the swift reply.<br>
With regards to the mdp setting<br>
<br>
<br>
> The proper setting for the "dihre" keyword is either "yes" or "no."<br>
<br>
How to I specify which dihedral I want to restrain and the force constant which I want to apply to it??<br>
<br>
</blockquote>
<br></div>
That's controlled in the topology. See the manual, section 4.3.3 and table 5.6.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Regards,<br>
Joanne<div><div></div><div><br>
<br>
On Fri, Mar 4, 2011 at 1:09 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Joanne Martin wrote:<br>
<br>
Hi, I'm a trying to calculate the PMF of a dihedral using<br>
Gromacs version 4.04.<br>
I have read through all posts on the mailing list regarding this<br>
query, and although Chris Neale did explain how to set the<br>
restraints for Gromacs 3, these options are now obsolete for<br>
4.04............ I get the following error ><br>
<br>
Ignoring obsolete mdp entry 'domain-decomposition'<br>
Replacing old mdp entry 'unconstrained-start' by 'continuation'<br>
Ignoring obsolete mdp entry 'dihre_tau'<br>
Ignoring obsolete mdp entry 'nstdihreout'<br>
Ignoring obsolete mdp entry 'nstcheckpoint'<br>
ERROR: invalid enum 'simple' for variable dihre, using 'no'<br>
<br>
<br>
The proper setting for the "dihre" keyword is either "yes" or "no."<br>
<br>
<br>
I have read Chris's paper from 2008 on alanine dihedrals but<br>
again this is done using Gromacs 3, and his tutorial for US in<br>
based on distance restraints.<br>
<br>
Basically I have two conformations of a sugar ( a starting<br>
conformation and an end conformation), and I want to generate a<br>
series of snapshots ie a reaction coordinate, from a "pulled"<br>
MD, for use in US.<br>
The pull code is only applicable to distance restraints, so how<br>
can I apply a restraint to the dihedral so that it will sample<br>
all dihedrals from the initial -180deg through to the end +180deg?<br>
<br>
<br>
You need to generate any intermediate structures at angles you wish<br>
to sample. There is no mechanism to enforce the rotation about a<br>
dihedral presently implemented in Gromacs.<br>
<br>
<br>
I would really appreciate if someone could explain to me, where<br>
I should set the restraints, as this is not clear from the manual.<br>
Also once the initial configurations are generated, is the below<br>
mdp option accurate for US of a dihedral ><br>
(query regarding distance option should this be direction??)<br>
<br>
<br>
The pull code is irrelevant here. Please do not attempt to apply my<br>
tutorial to your problem (beyond basic theory), as you will probably<br>
only frustrate yourself by doing so.<br>
<br>
When using a dihedral restraint, an energy term corresponding to the<br>
restraint should be written to the .edr file. I imagine you can<br>
plot these values as a function of the dihedral angle to extract the<br>
information you want.<br>
<br>
-Justin<br>
<br>
<br>
<br>
; Pull code<br>
pull = umbrella<br>
pull_geometry = *_distance_* ; can't get PMF with direction<br>
<br>
<br>
pull_dim = N N Y<br>
pull_start = yes pull_ngroups = 1<br>
pull_group0 = ? pull_group1 = ?<br>
pull_init1 = 0<br>
pull_rate1 = 0.0<br>
pull_k1 = 1000 ; kJ mol^-1 nm^-2<br>
pull_nstxout = 1000 ; every 2 ps<br>
pull_nstfout = 1000 ; every 2 ps<br>
<br>
<br>
<br>
<br>
Can someone please get back to me with any suggestions you may have,<br>
<br>
<br>
Kindest regards,<br>
Joanne<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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