Thanks a lot for your help guys, I think I found it. Best Regards, 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, 18:16 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]> 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://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 -----Ακολουθεί συνημμένο----- -- 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 -- 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 -----Ακολουθεί συνημμένο----- -- 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
-- 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
