Re: [gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-31 Thread Dommert Florian
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March

Re: [gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-31 Thread David van der Spoel
On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average

Re: [gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-31 Thread Dommert Florian
On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of

Re: [gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-31 Thread Nilesh Dhumal
Thanks Flo for detail reply. Is it possible to put PBC off during calculation of dipole moment autocorrelation function. I will run the simulation for 50ns ans try to save trajectroy of 0.02ps. Thanks NIlesh Nilesh On Thu, March 31, 2011 5:38 am, Dommert Florian wrote: On Thu, 2011-03-31 at

Re: [gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-31 Thread Dommert Florian
On Thu, 2011-03-31 at 08:53 -0400, Nilesh Dhumal wrote: Thanks Flo for detail reply. Is it possible to put PBC off during calculation of dipole moment autocorrelation function. No, thats the problem, because the volume of the system will increase and dipole density will decrease, this not

[gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-30 Thread Nilesh Dhumal
Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr

Re: [gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-30 Thread David van der Spoel
On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation

Re: [gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-30 Thread Nilesh Dhumal
Thanks. How can I take average. How much long I should run the simulation. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid).

Re: [gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-30 Thread David van der Spoel
On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh

[gmx-users] g_dipole: dipole moment autocorrelation function: Bug?

2011-03-22 Thread Nilesh Dhumal
Hello, I am trying to calculate the non normalized dipole moment autocorrelation function for water. I am using flexible spc water model (define=-DFLEX_SPC). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment

[gmx-users] g_dipole: dipole moment autocorrelation function: Bug?

2011-03-22 Thread Nilesh Dhumal
Hello, I am trying to calculate the non normalized dipole moment autocorrelation function for water. I am using flexible spc water model (define=-DFLEX_SPC). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment

[gmx-users] g_dipole: dipole moment autocorrelation function

2011-03-21 Thread Nilesh Dhumal
Hello, I am trying to calculate the non normalized dipole moment autocorrelation function for water. I am using flexible spc water model (define=-DFLEX_SPC). I am using gromacs 4.0.7 version. I run the simulation for 4 ns. I run the following command to calculate the dipole moment