amber-developers: nmode units

From: Ilyas Yildirim <>
Date: Thu, 11 Dec 2008 21:58:43 -0500 (EST)

Dear All,

I was trying to figure out what the units of the outputs of nmode
calculation is. Particularly, when NM=1 was set in mmpbsa calculation,
what is the units of TSXXX terms. The manual does not have any information
on this. In the file thermo.f, it is stated that

"the si system of units is used internally. conversion to units more
familiar to most chemists is made for output."

Almost at the end of the file, there is

   ! the units are now:
   ! e-- joules/mol
   ! c-- joules/mol-kelvin
   ! s-- joules/mol-kelvin

I guess the entropy calculated by nmode is in joules/mol-K. In the mm_pbsa
directory, the file mm_pbsa_output.txt states that TSXXX terms are T*S.

So, the units of the mmpbsa output for the entropy part is in joules/mol,
while the other terms (elec., vdw, PB, GB) are in kcal/mol, is this right?

It could be really useful if there was a file, which contained all the
units that are printed by each program. I think it might be really useful
for the users.


  Ilyas Yildirim, Ph.D.
  = Hutchison Hall B#10          - Department of Chemistry      =
  =                              - University of Rochester      =
  = 585-275-6766 (office)        -                              =
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Received on Fri Dec 12 2008 - 01:21:25 PST
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