[gmx-users] unit conversions

[Ramachandran G]

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.

with regards,
Rama

On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul <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>> 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
>
> ========================================
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-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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