On 11/6/12 1:21 PM, Ali Alizadeh wrote:
Dear Justin
Thank you for your reply
On 11/6/12 12:12 PM, Ali Alizadeh wrote:
Dear All users
1- Do these parameters strongly impact on my final results?
rlist
rcoulomb
rvdw
> Yes, potentially very strongly.
2- Are these parameters independent from type of system and only
dependent to type of the force fields?
>Yes.
3- I want to use gromos 45a3 ff but i do not know these parameters,
> Have you read the article in which 45A3 was derived? It
spells out precisely
> what you need to do.
Yes, i studied and i understand,
So as you said, I do not need to change rcoulomb and rvdw, is it true?
Change from what? You should use the settings described in the paper unless
there is newer evidence that the force field is equivalently (or more) effective
using some different settings.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
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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