[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly
jalemkul at vt.edu
Fri Oct 5 12:05:31 CEST 2012
On 10/5/12 5:18 AM, Bao Kai wrote:
> Hi, Justin,
> Thank you for your reply.
> It is a little weird and inconvienient that genbox does not update the No.
> of solute molecules. Is it designed in this way? Does it have any reason
> for that?
The principal function of genbox is to solvate systems, usually with water. The
other things it can do are added on, but the code is designed around the most
commmon usage. Insertion of molecules is not guaranteed to work, so if a user
specifies a number of molecules to add and then genbox cannot, then either it
will update with topology with the actual number inserted (which may disagree
with the command line, and users may ignore any failures and proceed) or the
number requested (which may then fail for the opposite reason). You can see how
it becomes a slippery slope to try to make software out-think the user.
> For my case, the inear, 3-atom model of CO2 works pretty well. I got the
> model from a paper from Zhenhao Duan. I guess I will use this model for
> the project before I get something wrong.
Good luck. Linear angles are generally not stable.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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