[gmx-users] unit conversions
Ramachandran G
gtrama at gmail.com
Sat Sep 18 04:01:57 CEST 2010
Thank you for your clarification.
Rama
On Fri, Sep 17, 2010 at 5:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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