Re: [gmx-users] g_dipoles: "index group is not a set of the whole molecules"

On 4/3/13 11:13 AM, Oleksandr Sushko wrote: Dear Gromacs users, can you help me please with next issue: I'm analysing solvation shell of water molecules around a protein. I use g_select to select different layers of water based on distance criteria. The output index file contains all the atoms

[gmx-users] g_dipoles: "index group is not a set of the whole molecules"

Dear Gromacs users, can you help me please with next issue: I'm analysing solvation shell of water molecules around a protein. I use g_select to select different layers of water based on distance criteria. The output index file contains all the atoms which satisfy the specified criteria. For som

[gmx-users] g_dipoles -g molecular center of mass issue

I am calculating the < cos > between molecular dipoles, and I am getting strange values for the molecular center of mass distance (r). So I ran a test on a simple dimer system: dips 4 1DIP C11 0.000 0.000 0.000 1DIP H11 1.000 0.000 0.000 1DIP C11

[gmx-users] g_dipoles with net charge

Dear gmx users: I am using gms 4.07, my system contains a protein with net charge and a plain,here I want to calculate the the angle between the dipoles of protein and the XY plain vs. time. What should I do? And is this way right: I define a positive center and a negative center, and define a

RE: [gmx-users] g_dipoles - averaging

300.00 K > and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 > Too less points for a fit. > > I am not sure, where to find the dipole moment for each of the four molecules. > > Many thanks > Andreas > > > > -Original Message- > >

RE: [gmx-users] g_dipoles - averaging

.@gromacs.org] > On Behalf Of Dommert Florian > Sent: 04 August 2011 12:31 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] g_dipoles - averaging > > On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote: > > Hello, > > > > Is there any

Re: [gmx-users] g_dipoles - averaging

On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote: > Hello, > > Is there any way to output the dipole moment averaged over all molecules or > for each molecule separately (and not the total dipole moment of the > simulation box) ? > Yes, the tool g_current decomposes the total dipole m

[gmx-users] g_dipoles - averaging

Hello, Is there any way to output the dipole moment averaged over all molecules or for each molecule separately (and not the total dipole moment of the simulation box) ? Apparently the dipole autocorrelation function can be obtained as an average over all molecules with the '-corr mol' option

[gmx-users] g_dipoles -slab option

Hi all, I am testing g_dipoles tool in GROMACS with a simple system containing only tip3p water molecules in a cubic box (6X6X6nm) with periodic boundary conditions in xyz. After the simulation is finished, using g_dipoles, I get the average epsilon=99.776 and the epsilon vs times also indicate th

Re: [gmx-users] g_dipoles + tpbconv

Nilesh Dhumal wrote: Hello, I have a system with a glucose molecule. I want to calculate the dipole moment of a particular OH in glucose molecule.I made an index file which have a group containing atoms. [ O8 ] 8 18 10 is oxygen no. and 20 is hydroen no. I'm assuming you mean 8 is O

[gmx-users] g_dipoles + tpbconv

Hello, I have a system with a glucose molecule. I want to calculate the dipole moment of a particular OH in glucose molecule.I made an index file which have a group containing atoms. [ O8 ] 8 18 10 is oxygen no. and 20 is hydroen no. But, if I try to use g_dipoles to get the dipole momen

[gmx-users] g_dipoles and index file

Hi, I was trying to calculate the dipole moment of part of my peptide. In other words, if I have a 10-residue peptide, I was interested in calculating the dipole-moment contribution of the backbone. So, I made an index file which have a group containing backbone atoms. But, if I try to use g_d

Re: [gmx-users] g_dipoles, average not the same as from g_analyze

Dear Emanuel, Please, check http://lists.gromacs.org/pipermail/gmx-users/2010-March/049316.html and Berk reply. I did never use -av (-a ?) option, maybe there is similar bug in average.xvg. Anyway last column of Mtot.xvg gives really correct norm of M_tot vector! Regards, Dmitri -

[gmx-users] g_dipoles, average not the same as from g_analyze

Dear gromacs users, Sorry but my last email was not correct. I have following question: With the use of the g_dipoles tool I have analysed the average dipole moment using following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -av average.xvg I think the option -av calculates the average of

[gmx-users] g_dipoles, average not the same as from g_analyze

Dear gromacs users, I have following question: With the use of the g_dipoles tool I have analysed the average dipole moment using following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -av average.xvg I think the option -av calculates the average of the dipole moment of the system I have ch

Re: [gmx-users] g_dipoles, take the normal of the computational box

On 2010-06-04 09.45, Emanuel Peter wrote: Dear Gromacs users, I have following question which regards to the g_dipoles tool. In order to get information about the total dipole moment of my protein I wrote following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -o Mtot.xvg -a average.xvg When

[gmx-users] g_dipoles, take the normal of the computational box

Dear Gromacs users, I have following question which regards to the g_dipoles tool. In order to get information about the total dipole moment of my protein I wrote following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -o Mtot.xvg -a average.xvg When I looked at the default options, the Z-axi

Re: [gmx-users] g_dipoles

e of a charged > molecule. > > Berk > > -- > Date: Tue, 17 Mar 2009 10:44:47 -0400 > Subject: Re: [gmx-users] g_dipoles > From: rams.c...@gmail.com > To: gmx-users@gromacs.org > > > Dear David, > > The peptide is having a -ve charge of 3. Though the compon

RE: [gmx-users] g_dipoles

s are possible for the dipole of a charged molecule. Berk Date: Tue, 17 Mar 2009 10:44:47 -0400 Subject: Re: [gmx-users] g_dipoles From: rams.c...@gmail.com To: gmx-users@gromacs.org Dear David, The peptide is having a -ve charge of 3. Though the components might dependent upon the orientation bu

Re: [gmx-users] g_dipoles

Dear David, The peptide is having a -ve charge of 3. Though the components might dependent upon the orientation but the average might be the same irrespective of the orientation I suppose. Ram. On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel wrote: > rams rams wrote: > >> Dear Users, >> >>

Re: [gmx-users] g_dipoles

rams rams wrote: Dear Users, I am trying to obtain the dipole moment of a 40 amino acid residue peptide using g_dipoles. I am getting a huge number (about 700 Debye). I expect it to be around 150 Debye (based on other studies). To make sure it I extracted a shapshot of the structure and obtai

[gmx-users] g_dipoles

Dear Users, I am trying to obtain the dipole moment of a 40 amino acid residue peptide using g_dipoles. I am getting a huge number (about 700 Debye). I expect it to be around 150 Debye (based on other studies). To make sure it I extracted a shapshot of the structure and obtained the dipolemoment u

Re: [gmx-users] g_dipoles gives wrong epsilon for SPC water

4, 2008 6:01:38 PM Subject: Re: [gmx-users] g_dipoles questions Semen Esilevsky wrote: Dear David, Thank you for reply! However there are still some question: Dear All, I have few questions about g_dipoles, which are not explained in the manual: 1) What method is used to calculate the epsi

[gmx-users] g_dipoles gives wrong epsilon for SPC water

ist for GROMACS users Sent: Wednesday, December 24, 2008 6:01:38 PM Subject: Re: [gmx-users] g_dipoles questions Semen Esilevsky wrote: > Dear David, > > Thank you for reply! However there are still some question: > > >>> Dear All, >>> I have few questions about

Re: [gmx-users] g_dipoles questions

Semen Esilevsky wrote: Dear David, Thank you for reply! However there are still some question: Dear All, I have few questions about g_dipoles, which are not explained in the manual: 1) What method is used to calculate the epsilon? Is there a reference which can be cited? Is it suitable for w

Re: [gmx-users] g_dipoles questions

Dear David, Thank you for reply! However there are still some question: >> Dear All, >> I have few questions about g_dipoles, which are not explained in the manual: >> 1) What method is used to calculate the epsilon? Is there a reference which >> can be cited? Is it suitable for water solutions

Re: [gmx-users] g_dipoles questions

Semen Esilevsky wrote: Dear All, I have few questions about g_dipoles, which are not explained in the manual: 1) What method is used to calculate the epsilon? Is there a reference which can be cited? Is it suitable for water solutions? In principle it is suitable for solutions of neutral molecul

[gmx-users] g_dipoles questions

Dear All, I have few questions about g_dipoles, which are not explained in the manual: 1) What method is used to calculate the epsilon? Is there a reference which can be cited? Is it suitable for water solutions? 2) I can't figure out the purpose of the option -enx. When I supply edr file with th

[gmx-users] g_dipoles questions

Dear All, I have few questions about g_dipoles, which are not explained in the manual (these questions are probably mostly to developers): 1) What method is used to calculate the epsilon? Is there a reference which can be cited? 2) I can't figure out the purpose of the option -enx. When I supply

[gmx-users] g_dipoles index file

Hi, I am trying to calculate the N-H dipole autocorrelation function of my protein using g_dipoles. The mentioned the atom numbers of these two in my index file. I have given the following command: g_dipoles -f md_minim_traj.trr -s MD_1BA4.tpr -P 2 -corr mol -c dipo_corr.xvg -b -e 1000 -n

Re: [gmx-users] g_dipoles output

Martin Höfling wrote: Hi Folks, I struggle with the output of g_dipoles, just to make sure that I understood it right: I select a subpart of my simulation and get the following output: Average volume over run is 216 Dipole moment (Debye) - Average = 0.4463 Std. Dev.

[gmx-users] g_dipoles output

Hi Folks, I struggle with the output of g_dipoles, just to make sure that I understood it right: I select a subpart of my simulation and get the following output: > Average volume over run is 216 > > Dipole moment (Debye) > - > Average = 0.4463 Std. Dev. = 0.5010 Err

[gmx-users] g_dipoles and charged molecules

Hi Berk sent some time ago a mail saying that g_dipoles can now handle charged molecules. Is this a recent version of gmx_dipoles.c (CVS)? Thanks. Best wishes George <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/ma

Re: [gmx-users] g_dipoles and fluctuation of the total dipolemoment

Guido Humpert wrote: Hello again, Thanks for your responses and suggestions. I think I understood the way epsilon is calculated in the source code, although I'm not very fermiliar with C. My question now is about your best bet of simulating the peptides in different concentration of water. What

Re: [gmx-users] g_dipoles and fluctuation of the total dipolemoment

Hello again, Thanks for your responses and suggestions. I think I understood the way epsilon is calculated in the source code, although I'm not very fermiliar with C. My question now is about your best bet of simulating the peptides in different concentration of water. What kind of simulation woul

Re: [gmx-users] g_dipoles and fluctuation of the total dipole moment

Guido Humpert wrote: Hello, I want to use g_dipoles to calculate the dielectric constant epsilon of peptides. The peptides contain between 20 and 40 Aminoacids and are solvated in dodecahedron water box. How can I define the -mu option in a system with a water solvated peptid? your problem is

Re: [gmx-users] g_dipoles and fluctuation of the total dipole moment

On Tue, 2006-08-01 at 12:39 +0200, Guido Humpert wrote: > Hello, > > I want to use g_dipoles to calculate the dielectric constant epsilon of > peptides. The peptides contain between 20 and 40 Aminoacids and are > solvated in dodecahedron water box. > How can I define the -mu option in a system wit

[gmx-users] g_dipoles and fluctuation of the total dipole moment

Hello, I want to use g_dipoles to calculate the dielectric constant epsilon of peptides. The peptides contain between 20 and 40 Aminoacids and are solvated in dodecahedron water box. How can I define the -mu option in a system with a water solvated peptid? How is the total dipole moment calculated

Re: [gmx-users] g_dipoles -slab option

+++ Bob Johnson [Wed, May 24, 2006 at 08:37:01PM -0400]: > for some reason and I can't interepret it. The first column is the position of > the water slab. I can only assume that column 2 is the dipole in the x > direction and column 3 is the dipole in the y direction and so on. Is that > correct?

[gmx-users] g_dipoles -slab option

Hello everyone, Water tends to align at a hydrophobic surface in a way to maximize H-bonds. Doing this leads to a dipole moment that is perpendicular to the surface (pointing away from the surface). Is this correct? I'm trying to verify this with a simulation. I have an uncharged surface in the xz