Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs version 4.04.<br><div class="gmail_quote">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>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>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><pre>; Pull code<br>pull = umbrella<br>pull_geometry = <b><u><span style="color: rgb(255, 0, 0);">distance</span></u></b> can't get PMF with direction<br>
pull_dim = N N Y<br>pull_start = yes <br>pull_ngroups = 1<br>pull_group0 = ? <br>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><font style="font-family: arial,helvetica,sans-serif;" size="2">Can someone please get back to me with any suggestions you may have</font><font size="2"><span style="font-family: arial,helvetica,sans-serif;">,</span><br style="font-family: arial,helvetica,sans-serif;">
</font><font style="font-family: arial,helvetica,sans-serif;" size="2">Kindest regards,<br>Joanne<br></font><br><br><br><br><br><br><br><br></pre><br>
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