Yes. I used the CHCL3BOX unit to build my slvent box. Is there any other
way to do this?
About C-Cl cleavage which I worried about,I remember I have eve run a MD
calculation and found the C-Cl bond to be cleaved. But I will do a test
claculation to make sure about this. Thank you so much.
Have a good day.
WJ
2009/1/5 David A. Case <case.biomaps.rutgers.edu>
> On Mon, Jan 05, 2009, WJ Ding wrote:
>
> > I built a solvent box of chloroform with tleap. When I visualized the pdb
> file
> > with VMD, it is found that the bond lengths of C-Cl even in the same
> molecule
> > are different (1.72-1.83 angstrom, I just cheked three molecules), which
> will
> > cause the C-Cl bond to be cleaved during the MD calculation. I do not
> think tt
> > is reasonable. Is there anyone who ever encountered this problem?
> What's
> > wrong with my solvent box?
>
> Bonds can never be cleaved in MD simulations -- why not minimize or run
> dynamics and see what happens.
>
> You didn't say how to created the solvent box, but my guess is that you
> used the CHCL3BOX unit. This file indeed has unequal C-Cl bond lengths
> -- it could be a snapshot from an MD simulation, although the magnitude
> of the deviations from ideality seems large.
>
> ...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Tue Jan 06 2009 - 15:24:40 PST
