On Wed, 17 Jan 2007, Nichols A. Romero wrote: NR> I am studying liquid nitromethane in a VERY small unit cell. There are only NR> 8 nitromethane molecules. NR> Already a problematic systems because the predominat interaction is vdW. It NR> is also at a very low density. NR> I run an NVT simulation for about 8 ps. I wrote a seperate program that NR> takes each nitromethane molecular NR> and calculation the translational kinetic energy, rotation kinetic energy of NR> the molecular (I recalculate NR> the moment of inertia at each step) and outputs a temperature based on those NR> quantities, e.g. T_trans=KE_trans/(3*N_mol) NR> NR> Anyhow, if the system is properly equilibrated, I would think that the NR> average T_trans and T_rot would be equal NR> to the imposed temperature by the thermostat. However, I am finding that it NR> is lower by 20-40% lower. My only NR> ideas are that: NR> 1. That this system requires ALOT more time to equilibrate. NR> 2. That initially all the energy must be getting locked into intramolecular NR> vibrations.
to get equipartitioning of the kinetic energy between all degrees of freedom, you will have to run individual thermostats on all of them (so-called massive nose-hoover chains). the transfer between rotational and translational degrees of freedom is generally slow and in smaller systems even more so. if you start from a classical pre-equilibration it is quite likely that you will provide a high excitation of the vibrational modes, due to bond lengths being different. rotations (i.e. orientation) should be less critical, particularly at lower density. please note, that using massive thermostatting will improve ergodicity, but also modifies your dynamics significantly (= win some, lose some ;-). also, and that may be even more important here, with only 8 molecules each molecule will 'see' the _same_ molecule on the 'both sides' in each direction, due to PBC. which should - to some degree - force all rotations to be somewhat synchronized across the whole 'crystal'. i have not looked at anything that small, but you can should be able to verify the impact of that effect from classical MD, where equilibration is not a problem. cheers, axel. NR> NR> Ideas anyone? -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
