<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>
<div>Thank you for your response.</div>
<div> </div>
<div>The column "Order of parameters and their units" of table 5.5 states that I have to include a value for n and the force constant k. </div>
<div>I tried it by simply setting k to 1:</div>
<div> [ bonds ]<br/>
;ai aj func n k<br/>
1 2 9 0 1</div>
<div> </div>
<div>it produces a similar error message (now for the angles instead of the bonds):</div>
<div>
<div>Fatal error:<br/>
Incorrect number of parameters - found 1, expected 2 or 4 for Tab. Angles.</div>
<div> </div>
<div>(I also added the n and k in the [angles] part like:</div>
<div>[ angles ]<br/>
; ai aj ak angleTyp n k<br/>
1 2 3 8 1 1</div>
<div>because of the fact that table 5.5 also states that I have to include a value for n and the force constant k for the angles.</div>
<div>)</div>
<div>Any idea if I have to secify further values? (Some which are not in table 5.5) </div>
<div>Or does anybody know the activator for such an error message?</div>
<div> </div>
<div>Thank you in advance!</div>
<div>Best,</div>
<div>Liz</div>
</div>
<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 15:33 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/>
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 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 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/>
> Dear all,<br/>
><br/>
> I am perfoming MD simulations of P3Ht chains and I would like to define the bonded as well as the nonbonded parameters using tables.<br/>
> Regarding the bonded parameters, there are no problems until now, as I simply wrote some additional lines in the mdp file (similar to this explanation: <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], [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 [...] 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 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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