Hi Justin, thanks so much for the swift reply.<br>With regards to the mdp setting<div class="im"><br><br>> The proper setting for the "dihre" keyword is either "yes" or "no."<br><br></div>How to I specify which dihedral I want to restrain and the force constant which I want to apply to it??<br>
<br>Regards,<br><font color="#888888">Joanne</font><br><br><div class="gmail_quote">On Fri, Mar 4, 2011 at 1:09 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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 class="im"><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, I'm a trying to calculate the PMF of a dihedral using Gromacs version 4.04.<br>
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 ><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>
</blockquote>
<br></div>
The proper setting for the "dihre" keyword is either "yes" or "no."<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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.<br>
<br>
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.<br>
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?<br>
<br>
</blockquote>
<br></div>
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.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I would really appreciate if someone could explain to me, where I should set the restraints, as this is not clear from the manual.<br>
Also once the initial configurations are generated, is the below mdp option accurate for US of a dihedral ><br>
(query regarding distance option should this be direction??)<br>
</blockquote>
<br></div>
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.<br>
<br>
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.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<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>
</blockquote>
<br></div>
-- <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>
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>
<br>
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