[gmx-users] g_analyze doubt

Dallas Warren Dallas.Warren at monash.edu
Tue Sep 27 00:06:11 CEST 2011

What have you tried with g_analyze so far?  What was your result?  Is it what you expect?  If not, why isn't it what you expect?

Trying something out is far faster and you learn more than waiting for a response from others that don't know exactly what you are doing.

At a first look, the command you want to run is

g_analyze -f data.xvg -ac autocorr.xvg

as you have a data file with time (x) and variable (y) data and you want the autocorrelation function of the variable data.  Have you tried that command?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of aiswarya pawar
Sent: Tuesday, 27 September 2011 3:11 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_analyze doubt


i read the help but i still didnt understand how do i compute the time series for this data, should i use this data as such for the input?

On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham <Mark.Abraham at anu.edu.au<mailto:Mark.Abraham at anu.edu.au>> wrote:
On 26/09/2011 5:10 PM, aiswarya pawar wrote:
HI Mark,

i have a .xvg data for the distance of two atoms in each time frame.

0.000000e+00  7.191033e-01
1.000000e+00  7.304224e-01
2.000000e+00  8.983867e-01
3.000000e+00  8.779736e-01
4.000000e+00  8.236583e-01
5.000000e+00  8.298320e-01
6.000000e+00  7.703011e-01
7.000000e+00  8.569826e-01
8.000000e+00  7.428180e-01
9.000000e+00  7.487683e-01
1.000000e+01  8.106729e-01
1.100000e+01  8.702058e-01
1.200000e+01  8.823072e-01
1.300000e+01  8.902194e-01
1.400000e+01  6.122664e-01
1.500000e+01  5.804662e-01
1.600000e+01  6.207849e-01
1.700000e+01  4.852896e-01
1.800000e+01  5.297776e-01
1.900000e+01  5.432515e-01
2.000000e+01  5.888653e-01
2.100000e+01  4.620140e-01

Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input.

Have you read g_analyze -h and tried it out?

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