Thanks a lot, Janne! I finally got it! Thanks for your inspiration! I added 1-4 pairs in [pairs] and then got the right values. I thought Gromacs would automatically find 1-4 pairs.
Lianqing On Thu, 7 Dec 2006, Janne Hirvi wrote: >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 > > _______________________________________________ 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
