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 > _______________________________________________ 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
