On 2011-03-27 19.23, Elisabeth wrote:
Thanks David for replying me. I appreciate your attention to
comment on the following short inquiries.
1- g_energy says:
you will need to give the number of constraints per molecule
–nconstr and
for water this is 3. Can you elaborate on how to set this option. When
constraints= all-bonds how to set -nconstr for a simlpe alkane for
instance? It refers to number of atoms of each molecule on which
constraints are applied?
Sorry but you have to do it yourself. Look up the equations and extract
the numbers from the energy file.
The other parameters may be problematic too.
2- Aside from heat capacities, does g_energy report the
following properties correctly?
Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
Isothermal compressibility: Vol, Temp
Adiabatic bulk modulus: Vol, Temp
3- Since volume appears for calculation of the above properties
, does this imply ONLY NPT results in these properties? (because
in NPT g_energy reports "volume").
4- For thermal expansion: I read one of your earlier messages
saying that enthalpy = Etot(total energy) +pv, [where Etot is
potential+kinetic (in g_energy list)]
and for pv , take ref_p and not measure p (that g_energy
reports). If the system is equilibrated to ref_p, then why not taking pv
from g_energy? you mean product of pv that g_energy gives is not
correct?
Many thanks for you time!
Best,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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