[email protected] wrote:
Hello, I want to set the density of the box (e.g. set 1 g/ml for
the water box). I use the density option in the editconf, then use the
genbox to generate the box, but the result of the density is not what I
setted. How can I do ?
The density of the box will be governed by how accurate the water model is in
reproducing experimental values. As far as I know, there isn't a water model
that gets density dead on. You could alter the box dimensions manually and use
a constant-volume ensemble, but whether or not it's appropriate to make such a
modification is questionable, since the water models are designed to reproduce
certain values with certain accuracy.
I have another question, I don't find the tip3p.gro and spce.gro
water model in the top file, only have the .itp document. if I want to
generate the TIP3P water box, how can I do, or where can I get the
tip3p.gro and spce.gro documents?
You don't need anything special, just coordinates for a 3-point water model and
sufficient equilibration:
http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file
-Justin
Thank you !
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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