Hi! I am not exactly sure but I think that there should be [pairs] section with all pairs named and the function number (=1) included but without any parameters which are then generated by Gromacs if "generate pairs" = "yes". You can check from the .log -file if you have any 1-4 Coulombic (or 1-4 Lennard-Jones) interactions included in your case.
Janne > Thanks, Janne! > > No, I tried not having [pairs] or having empty [pairs] because the manual > says it's not necessary if "generate pairs" = "yes". > > Lianqing > > > On Thu, 7 Dec 2006, Janne Hirvi wrote: > > >Hello! > > > >Just a simple question - Do you have [pairs]-section in your topology file? > > > >Janne > > > > > >> Dear GMX-users, > >> > >> Here are a followup and more details for my problem. I really hope to get > >> through this, so I can move on ... > >> > >> I report the electrostatic energy (Uq, kJ/mol) for a molecule using 3 > >> codes. > >> > >> 1. Gromacs 3.3 > >> [default] > >> 1 1 yes 0.5 FudgeQQ > >> > >> FudgeQQ [moleculetype] Uq > >> 0.0, 0.8333, or 1.0 mol 3 116.050 > >> 0.0, 0.8333, or 1.0 mol 2 -413.048 > >> > >> 2. DLPOLY with scaling factor of 0.83333 > >> Uq = -324.68 > >> > >> 3. My own code > >> Scaling factor Uq > >> 0.0 115.99 > >> 0.83333 -324.68 > >> 1.0 -412.81 > >> > >> Apparently, Gromacs gives the value without 1-4 interactions with "mol > 3", > >> and the value for full 1-4 interactions with "mol 2", regardless of > >> fudgeQQ. > >> > >> Did I not do something right when using Gromacs? > >> > >> Thanks A LOT for your help! BTW: the Gromacs website seems down. > >> > >> Lianqing > >> > >> On Wed, 29 Nov 2006, Lianqing Zheng wrote: > >> > >> >Dear GMX-users, > >> > > >> >I'm doing normal mode analysis for one molecule and found the calculated > >> >electrostatic energy (at t=0) doesn't change at all regardless of the > >> >value for fudgeQQ. (I used "1 1 yes 0.5 0.83333" for [default] and > >> >"molecule 2" for [moleculetype].) If I use "molecule 3", the value will > >> >change but is still independent of fudgeQQ. > >> > > >> >Any idea what the problem is? I'll be happy to send you the input files > if > >> >you need them. > >> > > >> >Thanks a lot! > >> > > >> >Lianqing _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
