Thank you Justin, actually, i have two parallel rigid plates that are free to move towards each other on the Y-axis (i used position restrain on Y and Z axes) later on i will umbrella sampling to obtain the plate-plate PMF at various distances from each other (thanks a lot for the helpful tutorial!)
so i will try bond type 6 as you suggested. up until now i observed , especially during the the NPT run ,that the atoms are fluctuating , and if the time step was 0.002psec or even 0.001 psec the system was very un-robust and the simulation explodes. (that is my main concern and the reason for my previous post) do you think bond type 6 will settle this? anyway, thanks a lot for the quick reply! Amir On Thu, Feb 4, 2010 at 7:32 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Amir Marcovitz wrote: > >> Hi, >> i'm simulating a surface in water and ions which is composed of 6X6 >> Carbon atoms arranged on a 2-d lattice. (using ffamber99) >> i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom >> (or some other spacing of choice..), and to maintain the surface rigid and >> planar >> for that i added to the [ bonds ] section at the topology file c0 values >> and force constants as following: >> [ bonds ] >> ; ai aj funct c0 c1 c2 c3 >> 1 2 1 3.400000e-01 3.744680e+05 >> 1 7 1 3.400000e-01 3.744680e+05 >> 2 3 1 3.400000e-01 3.744680e+05 >> .. >> and so on.. >> and similarly added 90 and 180 degrees bond angle constrains between >> triads of atoms in the surface according to their location. >> the thing is , i'm affraid my constraint of c0 of 3.4 Angst. is in some >> conflict with the definition of C-C bond length which is defined somewhere >> in the amber files (if i'm turning the constraint on co off the atoms >> approach each other and the spacing is lost) >> my questions are: >> a) do you think i should define a new dummy atom? and in which files >> should it be done? - i'm asking because i didn't find a clear answer in the >> manual >> b) is there any other bond function (what number?) which may ignore the >> definition of the C-C length and treat only the c0 constraint? >> > > Two options I can think of: > > 1. Why not position restrain your carbon lattices to parallel planes? > 2. Use bond type 6 to define a harmonic potential between the atoms you > want to restrain. If the two lattices are part of the same molecultype > definition (unclear from your post), then you can use distance restraints. > If they are separate molecules, however, you can't, and hence why bond type > 6 is a viable option. > > -Justin > > > if someone can answer or guide me to relevant sections in the manual i'll >> be most thankful! >> amir >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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