Hi, The number inserted depend on clashes with the input coordinates, so if you change those, don't be surprised if the output changes :-)
Mark On Wed, 3 May 2017 13:29 B Prakash <[email protected]> wrote: > On Wed, May 3, 2017 at 3:53 PM, Mark Abraham <[email protected]> > wrote: > > > Hi, > > > > On Wed, May 3, 2017 at 11:24 AM B Prakash <[email protected]> wrote: > > > > > Dear all, > > > am trying to do a simulation of a protein in methanol. Am using gromacs > > > 4.6.1. > > > > > > Do yourself a favour and for new work, install a version that isn't four > > years old, has extra bugs for free, and is unsupported ;-) > > > > Dear Mark, > thank you. I will do so. However, I was curious about the difference in the > number of methanol molecules added when all other parameters are same. > > > > > Am using the methanol box supplied in gromacs. In some of the > > > simulations, the box took nearly 10K (10040) methanol molecules. But in > > > others the number varied a little (10053). In editconf command, I tried > > to > > > center the protein in the simulation box. Is the variation in methanol > > > molecules due to minor changes in orientation of protein by editconf > and > > > genbox. Please correct. > > > > > > > Yes. There's an option to choose the maximum number of molecules added, > if > > you want a little more control. > > > > Mark > > > > > > > Regards, > > > Prakash. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to [email protected]. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
