[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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