[gmx-users] unit conversions
gtrama at gmail.com
Sat Sep 18 01:17:39 CEST 2010
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.
If anybody knows where i am making mistake please teach me. Thank you.
On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul <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).
> with regards,
> 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
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