Hi all,
I've been trying to sort this out (over on the main Amber list), and came to a point where I got a little stuck.
I have found that most of sander (and also pmemd) uses bars for its units, where pconv (in sander/runmd.f and pmemd/runmd.fpp) is set to 1.6604345d+04 * 4.184. In sander, I've updated this constant to use the values in constants.f; the conversion factor can be expressed in terms of Avogadro's number, the Joule-to-calorie conversion, and some orders of magnitude. So far, I haven't done the same for pmemd or pmemd.amba, because there doesn't seem to be the same dependence on a list of constants. In fact, in gbl_constants, I could only find a very few, such as pi.
At the moment, then, my sander (specifically, runmd) and my pmemd are out of step. Is it best to update the pmemd source so the same values of constants are used in both?
The other problem is that as well as pconv, both sander and pmemd define and use a "pressure_constant", which, unlike pconv, is a conversion factor appropriate for atmospheres. In sander's runmd, at least, this value is only used to calculate ener%pres(4), whatever that is, and even then only if iamoeba is non-zero and ipimd is zero. Can anyone clarify for me why this particular combination would use atms instead of bars for pressure, and whether I should fix it? As far as I can tell, this "feature" is also present in pmemd.
Thanks,
Ben
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Received on Mon Oct 11 2010 - 10:30:06 PDT
