----- Original Message ----- From: vinothkumar mohanakrishnan <kmvin...@gmail.com> Date: Monday, October 25, 2010 18:10 Subject: Re: [gmx-users] Reg; MD of DCE part II To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Hi mark > > The system was well equiulibrated and the average temperature > is 299.18 K and the pressure is 1.25 bar. ... and this means the system wants to contract (if this is an average pressure you've measured over a meaningful length of time). > I checked in the manual (gromacs version 4.0)l and there is no section like > 3.4.9 and i as well checked 7.3.15. OK, well look up in those chapters what GROMACS will do with pressure coupling (and plan to upgrade GROMACS). > i too know that when there is no pressure coupling the box size wont change. > what one will do if one wants to do in the NPT ensemble and wants to control > the box dimensions? Given dimensions for a system at a given temperature are only compatible with a certain equilibrium pressure. PV=nRT and all that. You have to equilibrate to your reference pressure before you can expect the volume to stay within a small fluctuation of an average, and cannot choose P, V and T arbitrarily. Mark
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