Thanks, Hess. The idea behind this order difference in coarse-grained scaling size is to keep solvent relative smaller to the target particle, or say after coarse-graining, solvent is still solvent and solute is still solute.
Regards, Jian -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Berk Hess Sent: Friday, July 20, 2007 3:17 PM To: [email protected] Subject: RE: [gmx-users] FW: rvdw >From: "Berk Hess" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users <[email protected]> >To: [email protected] >Subject: [gmx-users] FW: rvdw >Date: Fri, 20 Jul 2007 09:11:35 +0200 > > > > >>From: "Yin Jian" <[EMAIL PROTECTED]> >>To: "Berk Hess" <[EMAIL PROTECTED]> >>Subject: rvdw >>Date: Thu, 19 Jul 2007 12:53:00 +0800 >> >>Hi Dr Berk Hess, >> >>I am now using gromacs in simulation of coarse-grained model. As a >>multi-scale >> >>Coarse-graining, the LJ cutoff in gromacs is not fit this case. Since >>our model >> >>have particle with one order difference in their vdw radii. So the idea >>of fix is to >> >>change the original scheme at the source level. For example use a scalar >>variable >> >>to get the cutoff radius for each particle by multiplying the scalar to >>their own >> >>vdw radius. That would solve our problem easily. This dynamic LJ cutoff >>would >> >>be a second option relative to the current static (sinle-valued) cutoff. >> >>Do you think gromacs development group would like to make a change like >> >>that so that we may get our job done without too much bothering. >> >>Thanks in advance. >> >> >> >> >> >> >> >>Yin Jian (PhD) >> >>Research Staff, >> >>Singapore-MIT Alliance (SMA) >> >>National University of Singapore >> >>Singapore >> What do you mean with "does not fit the case"? You do not explain what you want exactly, but I think the current Gromacs setup would work. Or do you think you could gain performance with your proposed scheme? That would only be the case if you have regions with only small and only big particles. If the small and big particles are mixed, you would not gain much. In general it is a bad idea to have a coarse grained model with particles sizes that differ by an order of magnitude. Berk. _________________________________________________________________ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
