Thanks Justin. One last question, I wanted to make sure if zetting zero charge using tpbconv is identical to setting zero charges in top file.
I am concerned about the model to be inaccurate. Do these two models work similarly? Regards, On 28 July 2011 12:54, Justin A. Lemkul <[email protected]> wrote: > > > Juliette N. wrote: > >> Hello, >> >> I set zero charges to all atoms using the commands below: >> >> 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 >> >> So before doing mdrun md I add tpbconv command and use the out put >> *-ZERO_md.tpr for the mdrun md step. >> >> I did not touch mdp file to exclude >> >> coulombtype = >> rcoulomb-switch = 0 rcoulomb = 1.0 >> >> Although g_Energy is giving zero values for coulomb SR and 14 terms, CPU >> time doesnt change for the models with and without charges. >> I am just curious why run time is not changing given that electrostatics >> is the most time consuming calculation. Do I need to remove above lines from >> mdp? I am doubtful if electrostatic has been ignored from my model. >> >> > Turning off charges will not improve performance. The MD routine will > still calculate Coulombic interactions, but it will just waste time > producing all zeros. The only difference you might be able to see would be > PME vs. cutoff (the default coulombtype setting), with the latter being much > faster (but also much less accurate). > > The only way to exclude these interactions is to use energygrp_excl, but > that will exclude all nonbonded interactions, not just the electrostatics > terms. > > -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, Jennifer N.
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