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 gmx-users@gromacs.org 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
