Thank you Justin, but I ran a simulation before this one with GTP & it worked fine. GDP & GTP parameters are identical except for GDP having less atoms. This is why I can't understand why I don't get an integer charge while I did in my previous simulation.
Carla On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Carla Jamous wrote: > >> Hi, >> >> In order to run my simulation, I had to insert GDP parameters in ffamber94 >> (the force field I'm using). >> However, I'm having a problem with GDP charge. >> the charge of every charge group in top file should be an integer. But I'm >> getting a decimal charge which gives me naturally a decimal total charge of >> my molecule. >> I checked number of atoms, it's correct, their charge also. >> But it seems it's having trouble adding charges & giving an integer >> charge. >> Does anyone have an idea where is the source of the problem? >> >> > What is the charge? If it is a small difference between an integer and > your charge (i.e., the difference between +1.9999 and +2) then there is no > problem. The issue there is the inherent limitation of doing a lot of > floating-point operations to sum the total charge. If, however, you have a > charge of +1.9256 when you wanted +2, then your parameters are simply wrong. > > -Justin > > Thanks >> >> Carla >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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