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<pre>Dear all,
Regarding my question concerning the format of the [bonds] part of the topology file, I tried some new things:
Changing the [bonds] part in the topology to:
[ bonds ]
;ai aj func n
1 2 9 0</pre>
<div>
<div>for n=0 (and therefore the file: table_b0.xvg) produces this error message:</div>
<div> </div>
<div>Fatal error:<br/>
Incorrect number of parameters - found 1, expected 2 or 4 for Tab. Bonds.</div>
<div> </div>
<div>But the other error message reported in the first post vanished.</div>
<div>I would be really grateful if somebody could tell me how the line in the [bonds] part has to look like when using tabulated boned interactions.</div>
<div>Do I for example have to specify the force constant reported in the 4.2.14 section of the manual (by simply writing it behind the n) ?</div>
<div> </div>
<div>Best,</div>
<div>Liz</div>
<div> </div>
<div> </div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 04. August 2015 um 14:41 Uhr<br/>
<b>Von:</b> "Liz Bell" <LizBell@gmx.at><br/>
<b>An:</b> gromacs.org_gmx-users@maillist.sys.kth.se<br/>
<b>Betreff:</b> [gmx-users] tabulated bonded interaction functions</div>
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<pre>Dear all,</pre>
<div>
<pre>I am perfoming MD simulations of P3Ht chains and I would like to define the bonded as well as the nonbonded parameters using tables.
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>).
But how do I tell gromacs to use the information for [bonds], [angles]... (all the bonded potentials)... from table_b0.xvg for example.
The first line of the [bonds] section in my topology file looks like:
[ bonds ]
;ai aj func
1 2 9
Where 1 and 2 are the atoms and 9 is the function type.
Running grompp produces various of those mistakes:
</pre>
<div>
<div>No default Tab. Bonds NC types</div>
No default Lin. Angle types</div>
<div>No default Proper Dih. types</div>
<div> </div>
<div>I think Gromacs can not find the values that I defined in the table_b*.xvg, table_a*.xvg and table_d*.xvg.</div>
<pre>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.
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?</pre>
<div>Does anybody know how to adapt the topology file, or whether some additional lines are needed in the mdp files?<br/>
</div>
<div>Thank you very much in advance,</div>
<div> </div>
<div>Liz</div>
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</div>
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