hi... So there is no direct way to know the values to be used . however the last line is still unclear...
Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Fri, May 20, 2016 at 12:00 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Nikita, > > It's not like there's a range to take a minimum from. It's this with this > force field and that with another. Any deviation will alter the behaviour > of the force field, and you'll have to show that the result is valid, > either by running tests, or by referring to a paper that has results from > such tests. The most suitable value is probably the one used by groups that > have direct ties to the developing group(s). > > > Hope it helps, > > > Tsjerk > > > > On May 20, 2016 07:20, "Ms. Nikita Bora" <nik...@tezu.ernet.in> wrote: > > > Thanks Tsjerk > > > > That was really a good explanation. And it helped me out a lot. > > Still,I would like to know what are the standard values for these > > parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used. > > > > As earlier it was mentioned that with different force field different > > value is used so is there any link where i can get to know the minimum > cut > > off values for these parameters and which value should be used for which > > force field or condition > > > > thanks > > Nikita > > > > > > > > ---------------------------- Original Message > ---------------------------- > > > Subject: Re: simulation_time > > > From: "Ms. Nikita Bora" <nik...@tezu.ernet.in> > > > Date: Mon, May 16, 2016 9:42 am > > > To: nik...@tezu.ernet.in > > > > > > -------------------------------------------------------------------------- > > > > > > Respected Sir, > > > > > > Thanks for the reply. I would further like to know that according to > this > > > tutorial > > > ( > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html > > ) > > > the rvdw=rcoulomb=1 is used for the protein while according to this > > > tutorial > > > ( > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html > > ) > > > rvdw=rcoulomb=1.4 is used. why a different value for the simple protein > > > and protein-ligand complex is used?? > > > > > > > Different force fields, different settings. > > > > -Justin > > > > > > > > > > > ___________________ > > D I S C L A I M E R > > This e-mail may contain privileged information and is intended solely for > > the individual named. If you are not the named addressee you should not > > disseminate, distribute or copy this e-mail. Please notify the sender > > immediately by e-mail if you have received this e-mail in error and > > destroy it from your system. Though considerable effort has been made to > > deliver error free e-mail messages but it can not be guaranteed to be > > secure > > or error-free as information could be intercepted, corrupted, lost, > > destroyed, > > delayed, or may contain viruses. The recipient must verify the integrity > of > > this e-mail message. > > -- > > 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 gmx-users-requ...@gromacs.org. > > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.