2010/7/1 xrysostomos sfhsdfghsdfhsdgh <[email protected]> > Dear Gaurav > > Thanks a lot for your quick reply > > I have done also what you suggested but the result is the same. I mean that > I observe stronger adsorption of the polymers to the surface, when I > increased the values of c6 and c12 for Si in the [atomtypes], but > continue having original values in the *[ nonbond_params ].* > But in general, am I not able with gromacs to switch-off the LJ > interactions between the polymers and the substrate? > Is it possible to have this problems because I use NVT ensemble? >
You can switch-off all non-bonded interactions between a pair of energy groups by defining Energy group exclusions. Sec. 7.3.19 of the gromacs manual 4.0. -Gaurav > > Thanks again, Chrysostomos > --- Στις *Πέμ., 01/07/10, ο/η Gaurav Goel <[email protected]>*έγραψε: > > > Από: Gaurav Goel <[email protected]> > Θέμα: Re: [gmx-users] Problem with Lennard Jones cross terms > Προς: "Discussion list for GROMACS users" <[email protected]> > Ημερομηνία: Πέμπτη, 1 Ιούλιος 2010, 16:10 > > > By specifying both c6 and c12 to be zero, you've set both the attractive > and repulsive components of SI-OA, Si-CH2, Si-CH3 dispersion interactions to > zero. If you don't have any electrostatic repulsions in your system polymer > might be "attracted" to Silica substrate for entropic reasons...e.g., > centers of mass of Si and CH2 can overlap without any energy penalty. > > One solution will be to fix c6, c12 for SI-OA, Si-CH2, Si-CH3 to their > original values under *[ nonbond_params ] *and then do whatever you want > to do with the Si-Si interactions in [atomtypes]. > > -Gaurav > > 2010/7/1 xrysostomos sfhsdfghsdfhsdgh > <[email protected]<http://mc/[email protected]> > > > >> I am trying to simulate the following system: 5-layer FCC substrate >> consisting of Si particles which interact only with Lennard-Jones potential >> and vertical to the substrate I put polymer chains of (CH2-OA), starting >> from a distance of 0,4nm. >> >> What I want is to be able to manage completely independently the LJ >> interactions between the substrate and the polymers and not according to the >> combination rules, i.e. to have very very strong LJ interaction only between >> the Si particles but these to interact normally with the polymer chains. >> >> I use the Gromos-96 force-field. The initial values for the c6 and c12 >> parameters are the following: >> >> *[ atomtypes ]* >> >> name at.num mass charge ptype c6 >> c12 >> >> OA 8 0.000 0.000 A 0.0022619536 >> 1.505529e-06 >> >> CH2 6 0.000 0.000 A 0.0074684164 >> 3.3965584e-05 >> >> SI 14 0.000 0.000 A 0.01473796 >> 2.2193521e-05 >> >> >> >> *[ nonbond_params ]* >> >> i j func c6 c12 >> >> SI OA 1 0.0000000 0.00000000 >> >> SI CH2 1 0.0000000 0.00000000 >> >> SI CH3 1 0.0000000 0.00000000 >> >> >> >> What I did is to run 2 different simulations in NVT ensemble. In the * >> first*, I multiplied by 10 the c6, c12 values of Si in the [atomtypes ] and >> in the *second* I multiplied (the initial values again) by 100. In both >> cases I didn’t change the values on the [nonbond_params ]. >> >> I would expect that in both cases there should be no adsorption of the >> polymers in the substrate, since I change the interaction between the >> substrate and the polymers in the [nonbond_params ] equal to zero. >> >> What I observed is that after 50000 steps with 2 fs time step the polymers >> in the second case adsorbed to the surface. >> >> Can anybody help me or explain me why is this happening? >> >> >> >> Thanks in advance >> >> >> >> Chrysostomos >> >> >> -- >> gmx-users mailing list >> [email protected]<http://mc/[email protected]> >> http://lists.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]<http://mc/[email protected]> >> . >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -----Ακολουθεί συνημμένο----- > > -- > gmx-users mailing list > [email protected]<http://mc/[email protected]> > http://lists.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]<http://mc/[email protected]> > . > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > gmx-users mailing list [email protected] > http://lists.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 >
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