Dear amber experts,
I have simulated a box of water molecules (only water) with density 0.863 (g/cm^3) for 10ns time length. I have total about 1445 water molecules and total 10000 frames.
The purposes for doing this are two fold. First, is to calculate velocity autocorrelation function for water and compare the results with published work by Alder and Wainwright 1970 at given density value. Second, I have written Fortran90 code for calculating autocorrelation function (ACF) and want to check if my code calculates ACF correctly.
1) In my input parameter file, I used parameters (ntwv=-1,ioutfm=1) for print velocity in the trajectory files. Now I need some help to calculate the VACF using ptraj. How this can be achieved?
2) How I can get the velocity of a water molecule, lets say molecule number 1, starting from frame number one until frame number 10000? And velocity for water molecule number 2, starting from frame number one until frame number 10000? I want to collect velocity of a particular water molecule throughout simulation time length.
Appreciate any help in advance.
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 17 2012 - 04:30:05 PST
