[gmx-users] pressure in NVT simulations

[Anton Feenstra]

Ester Chiessi wrote:
> 
> David van der Spoel wrote:
>> I'm not sure g_density is correct, does it use the mass in the tpr file?
> 
> I suppose so.
[..]
> Experimental density is not very different from that of pure water. Calculated (by
> hand) density for the simulated system is 1.01 g/cm3.
> When I solvated the polymer by genbox, I obtained 1.0711g/cm3 and the same value
> was given by editconf.
> The more confident value seems that by g_density.

I know genbox does *not* get its mass from the .tpr file, so that is at least
the least reliable value.
The programs will tell you if it gets the mass not from the .tpr file, in
a warning message about 'mass based on atom names, not topes' and 'deviation
from real mass'.



-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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