From owner-chemistry _-at-_)ccl.net Sat Oct 1 10:22:00 2005 From: "Lubos Vrbka shnek#,#tiscali.cz" To: CCL Subject: CCL: Periodic boundary conditions Message-Id: <-29447-051001043455-9235-yZM5MJ7CuxR8oUvQcY8Kpw[*]server.ccl.net> X-Original-From: Lubos Vrbka Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 01 Oct 2005 09:33:09 +0200 MIME-Version: 1.0 Sent to CCL by: Lubos Vrbka [shnek_-_tiscali.cz] David Santos Carballal spectrum_dav*_*operamail.com wrote: > Sent to CCL by: "David Santos Carballal" [spectrum_dav[*]operamail.com] > Dear CCl members: > I am doing some molecular dynamics in TINKER. > I made a box of solvent (water) with the program xyzedit. > In the keyword file evoke keywords: rattle (the responsible of shake method in order to restrain O-H distances and angles in water); a-axis (to define lattice lenght); octahedron (to simulate a sistem closer to a sphere) and cutoff (to evaluate the integrals in a region smaller than the half of dimension of the box of solvent). > My system have 100 water molecules. > First of all I made a minimization with a conjugate gradient of 0.01. After it I run dynamic with the Beeman integration method and constant temperature (298K) and pressure (1 atm.). When the dynamic begins temperature stabilizes so fast but pressure is very high, it wuold be around 4000 atm. The pressure fall down at 1 atm. after 12000 steps, but the lattice length grow up so much, the initial lattice length was 14 angstroms and the final is 200 angstroms, with one consecuence: density fall down until 0.0010 grams/cc, that is desagree with water density. I use MM3 force field. > My question is I am using correctly periodic boundary conditions? > Why this results? if your initial system is ok and looks like it should look like then first thing i could think of: after minimization, do constant volume run first before switching to constant pressure to get somehow relaxed system. this might help a bit... -- Lubos _/./_"