On 5/17/12 12:58 PM, Lara Bunte wrote:
Hi
One cannot convert between these units, since kcal/mol is an energy term, and
kJ/(mol nm^2) is a force constant.
This confuses me, because in the paper where that constants are from is
written, I quote:
"Force constant k in kcal / mol calculated by DFT"
In my parametrization I have this values. Could you please explain this?
If this is a force constant for an angle, then it needs to simply be converted
to kJ/mol. See Table 5.5 of the manual for all force constant requirements.
Your original question is not solvable; one cannot convert kcal/mol to kJ/(mol
nm^2) as you cannot create a distance term out of nothing.
-Justin
Greetings and really thanks for your help
Lara
----- Ursprüngliche Message -----
Von: Justin A. Lemkul<jalem...@vt.edu>
An: Lara Bunte<lara.bu...@yahoo.de>; Discussion list for GROMACS
users<gmx-users@gromacs.org>
CC:
Gesendet: 18:52 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Force Constants and Unit Systems
On 5/17/12 12:25 PM, Lara Bunte wrote:
Hello
I never had contact with such units. Could you please help me and explain me
how to transform following units:
1.) kcal / mol --> kJ / (mol * nm^2)
One cannot convert between these units, since kcal/mol is an energy term, and
kJ/(mol nm^2) is a force constant.
2.) kcal / (mol * rad^2) --> kJ / (mol * rad^2)
The transformation between kcal and kJ requires a simple multiplication.
I have additionally some question to that: Both should be units of a force
constant. From Hooke's law F = -kx follows for me, that the unit of a force
constant is Newton N over distance m, in S.I. units kg/sec^2 (mass over time
square).
What is the correspondence between above from Hooke's law and that units of
force constants in molecular dynamics simulations?
Force is also expressed as kJ/(mol nm) - see Chapter 2 of the Gromacs manual.
Thus, since x is in units of nm (distance), then k has units of kJ/(mol nm^2).
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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