On 28/03/2011 11:29 PM, Nilesh Dhumal wrote:
I want to calculate the vibrational spectra of water by fourier transfom
of velocity autocorrelation function. TO study stretching and bending
vibration I have to use spc flexible water model.
You probably should to use a flexible water model, but making flexible a
model that was not designed to be flexible is not the best possible
approach. Look in the literature for water models that were parametrized
to be flexible, and preferably ones that are already known to reproduce
such properties.
Mark
On Fri, March 25, 2011 12:02 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am want to use flexible spc water model for my simulation.
Might I inquire as to why? SPC was parameterized to be rigid, and as has
been stated numerous times across the list, flexible water should not be
used.
I define=-DFLEX_SPC in my mdp and mentioned #include "spc.itp" in my
.top
file.
Does it correct?
Presumably. Check the post-processed topology that grompp gives you (-pp
argument).
-Justin
I am using gromacs 4.0.7 version.
Thanks
Nilesh
--
========================================
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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