[gmx-users] Rotational correlation function for water

[Praveen Kumar]

Hi,

I am calculating the rotational correlation time for water (SPC/E model) by
using the following command-

g_rotacf_mpi -f traj.trr -s pr.tpr -n ind.ndx -P 1  -o watr_ohh.xvg -fitfn
aexp


I am getting the correlation time

COR: Correlation time (plain integral from  0.000 to 2505.000 ps) =

*3.64607 ps*
I have define a group containing three atoms (OW HW1 HW2) in index file .
If, i take two atoms (OW and HW1, suppose if i want to calculate rotational
correlation time along O-H vector), then i am getting correlation time

COR: Correlation time (plain integral from  0.000 to 2505.000 ps) =  *4.80207
ps*

by using command-

g_rotacf_mpi -f traj.trr -s pr.tpr -n ind.ndx -P 1 -d -o watr.xvg -fitfn
aexp

It is reported 1.71 ps (by NMR experiment) and 2.0 ps< (by MD simulation
for SPC/E model).


Could anybody help me to understand, where am i doing wrong?

All these calculation are done from 5 ns production run (NVT ensemble) at
303 K.

Thanks
PRAVEEN KUMAR
Research scholar
INDIAN INSTITUTE OF SCIENCE
EDUCATION AND RESEARCH PUNE