Ramachandran G wrote:
I understood from the gromacs manual the units for epsilon and sigma are
KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom.
But when i checked for some atoms, the epsilon values are not matching.
i.e., for example i took the value of epsilon value of S from gromacs
1.8828 and divided by the conversion faction 4.184. The result is 0.45
but in MOIL the value is 0.25. I also checked some other atoms like
K,Na,Cl... there also the values does not match.
Are you comparing the same force fields? According to the MOIL documentation,
CHARMM is not implemented unless the user provides it. However, the epsilon
value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is
0.25, which I assume is where you're finding that value.
-Justin
If anybody knows where i am making mistake please teach me. Thank you.
with regards,
Rama
On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Ramachandran G wrote:
Hi gmx-users,
I would like to know the units conversion of epsilon, sigma
(from non-bonded, Van der Waal interaction) from Charmm or MOIL
to gromacs.
Thank you.
My guess would be that each of the respective manuals would discuss
whatever unit conventions are utilized. As far as Gromacs is
concerned, Chapter 4 contains information about such matters, as
well as Table 5.2 (and sections nearby).
-Justin
with regards,
Rama
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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