[gmx-users] LJ values conversion

[Justin Lemkul]

On Wed, Mar 27, 2013 at 9:57 AM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

> Thanks for the mail justin.
>
>
> In charmm27.ff, the value for bonded are in b0 and ko format, whereas the
> gromos uses them in different way? If so, how do i convert between them?
>
>
Please consult the manual, Chapters 4 and 5 for all the relevant equations
and implementation.


>
> The value i incorporated for specific atoms are from published journals.
> Thanks in advance.
>
>
I think you're missing my point though. Just because something is
published, doesn't mean you can use it for whatever purpose you like.
 People spend years working out properly balanced force fields, and if you
try to put in some new atom type, it upsets the balance of every
interaction.  You may be OK within the context of CHARMM (depending on what
the paper is, and what parameter set they modified), but I can guarantee
you that if you're trying to incorporate CHARMM parameters into GROMOS, all
you're doing is producing a pile of trash.  You can probably "make it work"
from a topology standpoint, but you shouldn't be doing it.  I hope my
perspective is clear; I'm trying to save you from wasted effort.

-Justin


>
>
> On 3/27/13 2:15 AM, ��������������� wrote:
> > Hello gmx,
> >
> >
> > I have LJ parameter value of C (epsilon = 0.0262 kcal/mol, sigma = 3.83)
> O (epsilon = 0.1591. sigma = 3.12) in charmm format and wants to use them
> in gromos43a1 or charmm27 force field in gromacs.
> >
> >
> > Could you tell me how do i convert them to gromacs format? Any examples
> plz.
> >
> >
>
> Equation 5.1 in the manual, or apply g_sigeps. Note that picking values of
> atoms randomly and inserting them into an existing force field is a great
> way to
> completely invalidate the force field. Atom types are balanced against one
> another. Making ad hoc changes means you're using an unvalidated parameter
> set,
> and any good reviewer is going to have serious issues with whatever data
> you
> produce.
>
> -Justin
>
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-- 

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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