Hi, There is a net attractive force from vdw interactions beyond the cut-off, which can be corrected for analytically *in the case of a homogeneous system*. There is a slight artifact arising from the use of cut-offs for non-homogeneous systems such as a protein in water. Often the same corrections are used for non-homogeneous systems. It all boils down to what you want to measure, if those artifacts are large enough to ruin your investigations.
13 nov 2012 kl. 17.46 skrev Zahra M: > thank you for your reply > I mean the distance between two proteins is more than the cut off value, > and in the other case the distance between two proteins is less than the cut > off value, > > Bests > -Zahra > > From: Erik Marklund <[email protected]> > To: Zahra M <[email protected]>; Discussion list for GROMACS users > <[email protected]> > Sent: Tuesday, November 13, 2012 2:08 PM > Subject: Re: [gmx-users] calculating lennard-jones interaction > > Hi, > > Could you rephrase the question? Distance larger than cut-off and cut-off is > less than distance seem equal by definition to me. > > Best, > > Erik > > 13 nov 2012 kl. 10.50 skrev Zahra M: > >> hi dear users >> wanna know if the distance between two species is more than the cut off >> radius of vdw interaction (in a SMD simulation), can we trust the simulation >> results? I mean what is the difference between this case and the situation >> that the cut off radius is lower than the distance between two species. >> bests. >> Zahra >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> 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 > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > [email protected] > http://www2.icm.uu.se/molbio/elflab/index.html > > > ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
