[gmx-users] unit conversions

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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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> 
> -- 
> Postdoctoral Research Scholar,
> Department of Chemistry,
> University of Nevada, Reno.

-- 
========================================

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

========================================