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.
Well, hopefully someone has proven that this should be possible. SPC was
designed to be rigid, not flexible:
http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html
-Justin
Nilesh
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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========================================
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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