[gmx-users] unit conversions

[Justin A. Lemkul]

Ramachandran G wrote:
> Thank you Justin,
>      You are right i am not comparing the same force field.
>    But i am still curious to know the conversion factor for epsilon from 
> MOIL to gromacs(charmm)force field.
> i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you.
> 

If you are not comparing the same force fields, you are not likely to get the 
same answer.  I thought I identified the fact that the value you are referring 
to corresponds to the MOIL implementation of OPLS-UA, which has no relationship 
whatsoever to the Gromacs implementation of CHARMM.

Dividing by 4.184 is the correct conversion factor for kcal->kJ.

-Justin

> with regards,
> Rama
> 
> On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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> <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 <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

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