Hello Justin, I am using tpbconv to set zero charges after em and after doing grompp_md.
grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq mdrun -s *-ZERO_md -o -c -e -x -v Do I need to use tpbconv after grompp_em? (before mdrun_em) Regards, On 28 July 2011 14:53, Justin A. Lemkul <[email protected]> wrote: > > > Juliette N. wrote: > >> Hi again, >> >> I am wondering if using tpbconv to set zero charges (case 1) works similar >> to when one sets zero atom charges in topology file from the very beginning >> (case 2). Do these two cases work similarly? >> >> > They should work identically. > > > I checked tpr file and I see that charges are set to zero. >> >> Can you please tell me what these lines mean? >> >> Does it refer to exclusion which is set to 3 in top file? >> >> > Yes. > > > excls[0][0..10]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10} >> excls[1][11..18]={0, 1, 2, 3, 4, 5, 6, 7} >> >> The number of these lines corresponds to atom numbers in the system. >> >> > They refer to the atom indices of the atoms in the [moleculetype], not the > consecutive numbering of the system (for the first molecule this will be the > same, but I thought I'd point that out). > > > -Justin > > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > 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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Thanks, J. N.
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