sorry Justin to get back to you gain. This means I have to set zero charges twice ( after grompp EM and grommp MD), since in grompp_md I am using topology file which sets actual charges again to all atoms. Do atoms charges affect EM configuration ?
Regards, On 28 July 2011 17:44, Justin A. Lemkul <[email protected]> wrote: > > > Juliette N. wrote: > >> 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) >> >> > If you want to do energy minimization with zero charges, then yes. > > -Justin > > Regards, >> >> >> On 28 July 2011 14:53, Justin A. Lemkul <[email protected] <mailto: >> [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 <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >> ==============================**__========== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <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> >> >> <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] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >. >> >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Thanks, >> J. N. >> >> > -- > ==============================**========== > > 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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