[gmx-users] g_dipole

Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. Due to the PBC, the function of the total dipole moment in time is not continuous. Can I removed PBC for g_dipole? Thanks Nilesh -- gmx-users mailing listgmx-users@gr

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

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 no

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

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

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 t

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

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 con

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

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 > > >

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

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 D

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

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 (ion

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

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 funct

[gmx-users] g_dipole: dipole moment autocorrelation function

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 -co

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

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 autocorrelati

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

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 autocorrelati

[gmx-users] g_dipole: dipole moment autocorrelation function

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 autocorrelati

Re: [gmx-users] g_dipole

On 3/7/11 9:52 PM, Nilesh Dhumal wrote: Hello, I am calculating vibrational spectra by calculating the Fourier transform of dipole moment correlation function. I have fortran code for the calculation of vibration spetra from the Fourier transform of dipole autocorrelation function. For better sp

[gmx-users] g_dipole

Hello, I am calculating vibrational spectra by calculating the Fourier transform of dipole moment correlation function. I have fortran code for the calculation of vibration spetra from the Fourier transform of dipole autocorrelation function. For better spectra I want to calculate the dipole autoc

Re: [gmx-users] g_dipole

the program actually reads all frames, but it computes the correlation up to half of the total length of the data (it is a homoscedasticity issue, you should read some textbook on time series analysis before you increase the output length using -acflen) best André On Thu, Feb 24, 2011 at 5:04 PM

Re: [gmx-users] g_dipole

Nilesh Dhumal wrote: How can I make prog. to read all frames. I already answered this. Use a proper setting for -acflen. -Justin On Thu, February 24, 2011 2:34 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am calculating dipole autocorrelation function for my system. I

Re: [gmx-users] g_dipole

How can I make prog. to read all frames. On Thu, February 24, 2011 2:34 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> I am calculating dipole autocorrelation function for my system. >> >> >> I run the simulation for 500ps and the plot of dipole autocorrelation >> function

Re: [gmx-users] g_dipole

Nilesh Dhumal wrote: Hello, I am calculating dipole autocorrelation function for my system. I run the simulation for 500ps and the plot of dipole autocorrelation function shows the results for 250 ps. I used the following command g_dipoles -f water.trr -s water.tpr -c -corr total Can anyon

[gmx-users] g_dipole

Hello, I am calculating dipole autocorrelation function for my system. I run the simulation for 500ps and the plot of dipole autocorrelation function shows the results for 250 ps. I used the following command g_dipoles -f water.trr -s water.tpr -c -corr total Can anyone tell whats the problem.

Re: [gmx-users] g_dipole

Nilesh Dhumal wrote: I used following command. g_dipoles -f 6.trr -s 6.tpr -corr total -normalize NO -c Its not working. Its giving following error Invalid command line argument: NO With arguments listed as -[no]option, the proper argument is "-nooption" so in your case, -nonormalize.

Re: [gmx-users] g_dipole

I used following command. g_dipoles -f 6.trr -s 6.tpr -corr total -normalize NO -c Its not working. Its giving following error Invalid command line argument: NO Nilesh On Tue, February 15, 2011 7:57 am, David van der Spoel wrote: > On 2011-02-15 13.51, Nilesh Dhumal wrote: > >> Hello, >> >> >

Re: [gmx-users] g_dipole

On 2011-02-15 13.51, Nilesh Dhumal wrote: Hello, I want to calculate dipole autocorrelation function without normalization. How can I calculate dipole autocorrelation function without normalization. I am using gromacs 4.0.7 version. Thanks Nilesh g_dipoles -h -- David van der Spoel, Ph.D.,

[gmx-users] g_dipole

Hello, I want to calculate dipole autocorrelation function without normalization. How can I calculate dipole autocorrelation function without normalization. I am using gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

Re: [gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/22/2010 04:35 PM, Carsten Kutzner wrote: > On Oct 22, 2010, at 4:14 PM, Chih-Ying Lin wrote: > >> >> Hi >> Sorry, I ask the same question again because i am not a decent person >> in this field. >> If possible, someone can give me a quick answer

Re: [gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

On Oct 22, 2010, at 4:14 PM, Chih-Ying Lin wrote: > > Hi > Sorry, I ask the same question again because i am not a decent person in this > field. > If possible, someone can give me a quick answer while i am trying to get > understanding the source codes. > My basic understanding is that Gromacs

[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

Hi Sorry, I ask the same question again because i am not a decent person in this field. If possible, someone can give me a quick answer while i am trying to get understanding the source codes. My basic understanding is that Gromacs has other approach of calculating dipole moment instead of the foll

Re: [gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

On 2010-10-22 00.49, Chih-Ying Lin wrote: Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not

[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not consider counter ions to calculate the di

[gmx-users] g_dipole ? =>salt-molecule => the relative position of counter ions to the rest of salt-molecule matters ???

HI As Timo M.D. Graen described "As long as the system is neutral, the reference point will not affect the calculation result of the dipole moment for the system." On the other hand, I also play around the small salt-molecule as Timo M.D. Graen suggested. "take two ions for a start, Na+ and Cl-,

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

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 tran

[gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. The PBC is considered. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here "A" are a string of atoms, most of them are carbons

Re: [gmx-users] g_dipole ? => salt molecule in water => what is the the displacement vector pointing from the negative charge to the positive charge?

reconsider your statement about the displacement vector. You should try to understand the concepts of vectors and reference points first. It is absolutely mandatory to do so before calculating dipole moments of charged systems. It might also be wise to use a small test system to practice on. Fo

Re: [gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

Hey Lin, Did you consider PBC? Also, I wouldn't include the bromide if I were you, as it just adds noise, because it can move around freely. You seem to be interested in the change in dipole moment in the cation only, anyway. Cheers, Tsjerk On Oct 21, 2010 7:02 AM, "Chih-Ying Lin" wrote: HI

[gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here "A" are a string of atoms, most of them are carbons. For the cis-structur

[gmx-users] g_dipole ? => salt molecule in water => should I include counter ions in my calculation?

HI 48.0 sum of q_i x_i x_i is the atomic position. For the salt molecule in water, should I include counter ions in my calculation ? Or, only the rest of the salt molecule except the counter ions? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

[gmx-users] g_dipole ? => salt molecule in water => what is the the displacement vector pointing from the negative charge to the positive charge?

Hi molecule dipole is 48.0 sum of q_i x_i based on the following two websites, *x_i * is the displacement vectorpointing from the negative charge to the positive charge. what about the x_i for the salt-molecule, which dissociates into one co

Re: [gmx-users] g_dipole ? => what is the bond length of the ionic bond in the dipole moment calculation?

On 2010-10-20 06.06, Chih-Ying Lin wrote: Hi molecule dipole is 48.0 sum of q_i x_i x_i the bond length for covalent bond. No. x_i is the atomic position. but what is "x_i" for salt-molecule? For salt-molecule, the ionic bonds are broken in water solvent and the counter ions are spread

[gmx-users] g_dipole ? => what is the bond length of the ionic bond in the dipole moment calculation?

Hi molecule dipole is 48.0 sum of q_i x_i x_i the bond length for covalent bond. but what is "x_i" for salt-molecule? For salt-molecule, the ionic bonds are broken in water solvent and the counter ions are spread among the water. What is the "x_i" of the ionic bond in the dipole moment calculati

[gmx-users] g_dipole ? => ionic bond => how to determine the direction of ionic bond dipole moment ?

Hi molecule dipole is 48.0 sum of q_i x_i For a multiple-atoms molecule, the dipole moment of a covalent bond is a vector, parallel to the bond axis, For a multiple-atoms molecule, which includes a ionic bond, how to determine the direction of ionic bond dipole moment in theory ? How does Gromacs

Re: [gmx-users] g_dipole ? => Calculate bond dipole moment for a molecule of multiple atoms by hand?

Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long a

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

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 a

[gmx-users] g_dipole ? => Calculate bond dipole moment for a molecule of multiple atoms by hand?

Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment [image: \mu = \delta \, d]. The bond dipole is modeled as +δ -- δ- with a distance *d* between the partial charges +δ and δ-. For a complete molecule the total mo

[gmx-users] g_dipole ? => dipole moment ?

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? 2. Is q_i = partial charge or charge on the atoms / united atoms? 3. Is x_i = the distance between the mass center of atom fr

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

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 test

[gmx-users] g_dipole ? => dipole moment ?

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 aro

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

-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 Av

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

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 al

[gmx-users] g_dipole ? => dipole moment ?

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?

[gmx-users] g_dipole for spce

Dear all, I tried to use g_dipole for a SPC/E water system and I got these results. - Dipole moment (Debye) - Average = 2.3506 Std. Dev. = 0.0143 Error = 0.0001 The following averages for the complete trajectory have been calculat