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<p style="margin: 0px;">Thank you both.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I have set up soft core parameters for this test. All I want is an actual test to work at this point.<span></span></p>
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On September 15, 2010 at 5:31 PM "Justin A. Lemkul" <jalemkul@vt.edu> wrote:<br />
<br />
><br />
><br />
> TJ Mustard wrote:<br />
> ><br />
> ><br />
> > I started a small 2 nucleic acid system for FEP testing. As well as<br />
> > turning on fep, I set RNA_Chain_A as the couple-moltype. I also set<br />
> > couple-lambda0 and couple-lambda1 to vdw-q and none respectively. I then<br />
> > began a "steep" mdrun and got this error:<br />
> ><br />
> > <br />
><br />
> Unrelated to your error, but potentially problematic: decoupling both LJ and<br />
> Coulombic interactions simultaneously might lead to convergence problems.  See<br />
> the free energy tutorial for information.<br />
><br />
> ><br />
> > <br />
> ><br />
> > Program mdrun, VERSION 4.5<br />
> > Source code file: topsort.c, line: 112<br />
> ><br />
> > Fatal error:<br />
> > Function type Improper Dih. not implemented in ip_pert<br />
> > For more information and tips for troubleshooting, please check the GROMACS<br />
> > website at http://www.gromacs.org/Documentation/Errors<br />
> ><br />
> > <br />
> ><br />
> > I have searched for this on google and found nothing. Do I need an<br />
> > Improper Dihedral section in my top/itp file? I have ran this same<br />
><br />
> If you have planar compounds (like nucleic acids), you likely have a [dihedrals]<br />
> directive that corresponds to the impropers.  Check the function types.<br />
><br />
> > system with fep off and it runs perfectly.<br />
> ><br />
> > <br />
><br />
> It looks like the code in topsort.c does not deal with both F_IDIH and F_PIDIH,<br />
> which maybe (?) is the source of the problem.  Normal harmonic impropers can be<br />
> perturbed, i.e.:<br />
><br />
>      case F_IDIHS:<br />
>          bPert = (ip->harmonic.rA  != ip->harmonic.rB ||<br />
>                   ip->harmonic.krA != ip->harmonic.krB);<br />
>          break;<br />
><br />
> Perhaps there's something about your impropers that doesn't allow for<br />
> perturbation.  At the very least, a test for F_PIDIH is missing, but I'll defer<br />
> to the developers to weigh in on the need for a fix.<br />
><br />
> -Justin<br />
><br />
> ><br />
> > Any help is much appreciated.<br />
> ><br />
> > <br />
> ><br />
> > TJ Mustard<br />
> > Email: mustardt@onid.orst.edu<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 />
> jalemkul[at]vt.edu | (540) 231-9080<br />
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br />
><br />
> ========================================<br />
> --<br />
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><br />
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<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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