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.
