David, Thanks for the quick reply.
Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg The output file created includes three columns. 1. time ( ps) 2. shear viscosity (3) I assume it is bulk viscosity. It seems, the unit given is cp. ( 1cp= 1* 10¯3 Pascal Second). The bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two order of magnitude. I wonder whether I have done anything wrong while specifying the frequency of saving energy file. I have saved the energy file in every 2ps. Isn´t that enough for a simple system like water? OR should I have to save trajectories in every 5fs as suggested by one in a previous post. I post the first 20 lines of the output file. ------------------------------------------------------------------- # This file was created Thu Mar 12 16:20:09 2009 # by the following command: # g_energy -f water.edr -vis test.xvg # # g_energy is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @ title "Bulk Viscosity" @ xaxis label "Time (ps)" @ yaxis label "\8h\4 (cp)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Shear" @ s1 legend "Bulk" 1.99203 9.6633 96.3893 3.98406 11.1625 98.1365 5.9761 12.6631 99.838 7.96813 13.4652 101.366 9.96016 13.7012 100.249 ------------------------------------------------------------------------- regards, Jes On Thu, 12 Mar 2009 David van der Spoel wrote : >JMandumpal wrote: >>Dear GROMACS users, >> >> As explained in the manual ( page 139, section >> 6.5/3.3.3) I would like to calculate viscosity of my system ( water) using >> g_energy. I opted (40 Mu-X ) from the g-energy selection. But the unit >> written on the Y axis of the corresponding xvg file is (kJ mol\S-1\N). I >> think GROMACS uses SI unit , which is Pa-Second in the case of viscosity. >> Then why is this discrepancy.? Or did I make any mistake? >> >Mu is the dipole (in Debye). The units of these things are incorrect for >everything that is not an energy. This will be fixed in the next gmx version. >g_energy -h tells you what to do: > >g_energy -f ener -vis viscosity > >> >>------I give the command on the prompt: >> >>g-energy -f ener.edr - o viscosity.xvg ; >>then chose option 40 ( Mu-X). >> >>system details: >>****************** >>My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at >>150K, the ensemble is NPT. The version I am using is 3.3.3
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