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

[gmx-users] g_dipole ? = dipole moment = trans-structure is more hydrophobic than the cis-structure ?

2010-10-21 Thread Chih-Ying Lin
Hi In one paper, the salt-molecule has two structures, trans and cis. The sentence in the paper is that trans-structure is more hydrophobic than the cis-structure without providing the value of the dipole moment. I wonder know if the value of dipole moment is the main indicator to decide if

Re: [gmx-users] g_dipole ? = dipole moment ?

2010-10-19 Thread David van der Spoel
On 2010-10-19 02.01, Chih-Ying Lin wrote: Hi From David = dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. 1. What does the coefficient 48.0 represent? Unit conversion from e nm to D. 2. Is q_i = partial charge or charge on the

Re: [gmx-users] g_dipole ? = dipole moment ?

2010-10-18 Thread David van der Spoel
On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I

Re: [gmx-users] g_dipole ? = dipole moment ?

2010-10-17 Thread Florian Dommert
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/16/2010 10:28 PM, David van der Spoel wrote: On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average

[gmx-users] g_dipole ? = dipole moment ?

2010-10-17 Thread Chih-Ying Lin
HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment

[gmx-users] g_dipole ? = dipole moment ?

2010-10-16 Thread Chih-Ying Lin
Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time?

Re: [gmx-users] g_dipole ? = dipole moment ?

2010-10-16 Thread David van der Spoel
On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for