<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>Hello,
<div>
<div>there was indeed a mistake in my [angles] entry but the basic implementation works like described below.</div>
<div>Grompp now works perfectly. Thank you very much for confirming me that the basic implementation was correct.</div>
<div> </div>
<div>But now I have another question: How do I include the tables of the bonded interaction functions in mdrun?</div>
<div>Simply</div>
<div>"mdrun"</div>
<div>does not work. Using the command "-table" like</div>
<div>"mdrun -table table_b0.xvg table_b1.xvg table_b2.xvg table_a0.xvg table_a1.xvg table_a2.xvg table_a3.xvg table_d0.xvg table_d1.xvg table_d2.xvg table_d3.xvg"</div>
<div>or</div>
<div>"mdrun -table table*.xvg"</div>
<div>does not work neither.</div>
<div>Anybody an idea?</div>
<div> </div>
<div>Thanks,</div>
<div>Liz</div>
<div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 04. August 2015 um 16:07 Uhr<br/>
<b>Von:</b> "Mark Abraham" <mark.j.abraham@gmail.com><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> Re: [gmx-users] tabulated bonded interaction functions</div>
<div name="quoted-content">Hi,<br/>
<br/>
I believe your [angles] entries should work, but I've never tried it, and I<br/>
could easily believe that a bug exists. This is code that the developers<br/>
rarely use.<br/>
<br/>
If you're confident you got that output from a correctly-formed [angles]<br/>
section, then please open a report at <a href="http://redmine.gromacs.org" target="_blank">http://redmine.gromacs.org</a>, attach<br/>
the necessary files in a tarball and we can get to the bottom of it.<br/>
<br/>
Thanks,<br/>
<br/>
Mark<br/>
<br/>
On Tue, Aug 4, 2015 at 3:55 PM Liz Bell <LizBell@gmx.at> wrote:<br/>
<br/>
> Thank you for your response.<br/>
><br/>
> The column "Order of parameters and their units" of table 5.5 states that<br/>
> I have to include a value for n and the force constant k.<br/>
> I tried it by simply setting k to 1:<br/>
> [ bonds ]<br/>
> ;ai aj func n k<br/>
> 1 2 9 0 1<br/>
><br/>
> it produces a similar error message (now for the angles instead of the<br/>
> bonds):<br/>
> Fatal error:<br/>
> Incorrect number of parameters - found 1, expected 2 or 4 for Tab. Angles.<br/>
><br/>
> (I also added the n and k in the [angles] part like:<br/>
> [ angles ]<br/>
> ; ai aj ak angleTyp n k<br/>
> 1 2 3 8 1 1<br/>
> because of the fact that table 5.5 also states that I have to include a<br/>
> value for n and the force constant k for the angles.<br/>
> )<br/>
> Any idea if I have to secify further values? (Some which are not in table<br/>
> 5.5)<br/>
> Or does anybody know the activator for such an error message?<br/>
><br/>
> Thank you in advance!<br/>
> Best,<br/>
> Liz<br/>
> *Gesendet:* Dienstag, 04. August 2015 um 15:33 Uhr<br/>
> *Von:* "Mark Abraham" <mark.j.abraham@gmail.com><br/>
> *An:* gmx-users@gromacs.org<br/>
> *Betreff:* Re: [gmx-users] tabulated bonded interaction functions<br/>
> Hi,<br/>
><br/>
> Yes you have to specify k. That detail is in table 5.5, to which that<br/>
> section refers you.<br/>
><br/>
> Mark<br/>
><br/>
> On Tue, Aug 4, 2015 at 3:26 PM Liz Bell <LizBell@gmx.at> wrote:<br/>
><br/>
> > Dear all,<br/>
> > Regarding my question concerning the format of the [bonds] part of the<br/>
> topology file, I tried some new things:<br/>
> > Changing the [bonds] part in the topology to:<br/>
> > [ bonds ]<br/>
> > ;ai aj func n<br/>
> > 1 2 9 0<br/>
> ><br/>
> > for n=0 (and therefore the file: table_b0.xvg) produces this error<br/>
> > message:<br/>
> ><br/>
> > Fatal error:<br/>
> > Incorrect number of parameters - found 1, expected 2 or 4 for Tab. Bonds.<br/>
> ><br/>
> > But the other error message reported in the first post vanished.<br/>
> > I would be really grateful if somebody could tell me how the line in the<br/>
> > [bonds] part has to look like when using tabulated boned interactions.<br/>
> > Do I for example have to specify the force constant reported in the<br/>
> 4.2.14<br/>
> > section of the manual (by simply writing it behind the n) ?<br/>
> ><br/>
> > Best,<br/>
> > Liz<br/>
> ><br/>
> ><br/>
> > *Gesendet:* Dienstag, 04. August 2015 um 14:41 Uhr<br/>
> > *Von:* "Liz Bell" <LizBell@gmx.at><br/>
> > *An:* gromacs.org_gmx-users@maillist.sys.kth.se<br/>
> > *Betreff:* [gmx-users] tabulated bonded interaction functions<br/>
><br/>
> ><br/>
> > Dear all,<br/>
> ><br/>
> > I am perfoming MD simulations of P3Ht chains and I would like to define<br/>
> the bonded as well as the nonbonded parameters using tables.<br/>
> > Regarding the bonded parameters, there are no problems until now, as I<br/>
> simply wrote some additional lines in the mdp file (similar to this<br/>
> explanation:<br/>
> <a href="http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials" target="_blank">http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials</a>).<br/>
> > But how do I tell gromacs to use the information for [bonds],<br/>
> [angles]... (all the bonded potentials)... from table_b0.xvg for example.<br/>
> ><br/>
> > The first line of the [bonds] section in my topology file looks like:<br/>
> > [ bonds ]<br/>
> > ;ai aj func<br/>
> > 1 2 9<br/>
> > Where 1 and 2 are the atoms and 9 is the function type.<br/>
> > Running grompp produces various of those mistakes:<br/>
> ><br/>
> > No default Tab. Bonds NC types<br/>
> > No default Lin. Angle types<br/>
> > No default Proper Dih. types<br/>
> ><br/>
> > I think Gromacs can not find the values that I defined in the<br/>
> > table_b*.xvg, table_a*.xvg and table_d*.xvg.<br/>
> ><br/>
> > The section 4.2.12 in the gromacs manual tells "...for a bond with n=0<br/>
> [...] the table is read from the file table_b0.xvg.<br/>
> > But where do I have to specify that the atoms 1 2 have the bonds with<br/>
> n=0, with the information provided in the table_b0.xvg?<br/>
> ><br/>
> > Does anybody know how to adapt the topology file, or whether some<br/>
> > additional lines are needed in the mdp files?<br/>
> ><br/>
> > Thank you very much in advance,<br/>
> ><br/>
> > Liz<br/>
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