[gmx-users] Top file modification

[Justin Lemkul]

On Tue, Mar 19, 2013 at 1:07 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

>
>
>  Dear users,
>
> I modified my top file, because I didn't want some bonds. So I deleted
> them and changed charges on some atoms.
> I want to go on with such a top file, however I am not sure that these
> changes are implemented properly or not. Would you please let me know if
> what I did is right or not?
>
> And how would I be sure about the proper modifications?
>
>
Making ad hoc changes to topologies or force fields is generally a bad idea
unless you have thoroughly validated what you are doing with a correct
parameterization procedure.  What you've described above (especially given
the lack of specificity) sounds very dangerous. If you want advice, be
specific as to exactly what you are doing. It is your job to convince a
skeptical audience (e.g., reviewers) that what you're doing makes sense and
thus you must have strong justification for it. "Somebody on the Internet
told me it was OK" is generally not an acceptable defense ;)

-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

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