<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>
<div>
<div>Dear Andrish Reddy,</div>
<div> </div>
<div>Dont know if it works but I have for small molecules just put all the parmeters within the .top file right below the defaults, instead of user defined tables, and removed the "forcefieldX/SPC.itp" or equivalent section so it doesn't loop, but dont know if it works in your case. Just a quick suggestion to try, as I parse e-mails. Smone else probably has better answeres though...</div>
<div> </div>
<div>Stephan</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> Mittwoch, 22. Mai 2013 um 16:09 Uhr<br/>
<b>Von:</b> "Andrish Reddy" <areddy@csir.co.za><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> [gmx-users] C6 & C12 parameters for non-bonded interactions using tables</div>
<div name="quoted-content">Greetings,<br/>
<br/>
I am trying to use tabulated potentials for the VdW interactions between<br/>
TIP5P water molecules.<br/>
I have tested my topology file to make sure that it gives reasonable results<br/>
with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 ,<br/>
C12=4*eps*sig^12. I am able to match the energies with an identical run not<br/>
using look-up tables. The problem comes when I want to include the C6 & C12<br/>
parameters within the table. This is needed for dealing with more complex<br/>
multi-parameter potential functions.<br/>
<br/>
I tried testing this with the standard Lennard-Jones potential. Setting<br/>
g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my<br/>
table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)]<br/>
<br/>
I set vdw-type = user in my mdp file and modified my topology so that:<br/>
[ defaults ]<br/>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br/>
1 1 yes 0.5 0.8333<br/>
<br/>
[ atomtypes ]<br/>
; name at.num mass charge ptype C6 C12<br/>
OW_tip5p 8 16.00 0.0000 A 1.00000e+00 1.00000e+00<br/>
<br/>
Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg<br/>
and C6=4*eps*sig^6 , C12=4*eps*sig^12<br/>
The run proceeds fine with no warnings or errors, but the LJ and Potential<br/>
energies are an order of magnitude higher than when using the standard<br/>
table. I don't understand why I am not able to reproduce the results by this<br/>
method?<br/>
<br/>
Thanks,<br/>
Andrish<br/>
<br/>
<br/>
<br/>
<br/>
--<br/>
View this message in context: <a href="http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html" target="_blank">http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html</a><br/>
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.<br/>
--<br/>
gmx-users mailing list gmx-users@gromacs.org<br/>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br/>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br/>
* Please don't post (un)subscribe requests to the list. Use the<br/>
www interface or send it to gmx-users-request@gromacs.org.<br/>
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a></div>
</div>
</div>
</div></div></body></html>