RE: [gmx-users] g_vanhove output
I think I coded this all correctly, but the last time I used it was years ago. In 3D you could plot G(x), G1(y) and G(z), which are equal for an isotropic liquid. -or plots g(r) which is 2 pi r^2 G(r) Berk From: c...@purdue.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] g_vanhove output Date: Tue, 4 Aug 2009 11:02:51 -0400 Thanks Berk.I did look at the code, but it is not that easy to understand.My conclusion comes from this:for a diffusive regime, G(r) should be a gaussian function, with the diffusioncoefficient characterizing the width.I did some tests, and I could match both curves (one from g_vanhove and the other from the diff.coef) only if I multiply the output of g_vanhove by r and normalizing again, which makes little sense to me.It would be ok to output G(r) or r^2*G(r), but to output r*G(r) seems a mistake Thanks again,Marcelo PS: I did consider the spherical integration. On Aug 4, 2009, at 10:41 AM, Berk Hess wrote:Hi, You can look at the code yourself :) I coded this and -or (which I assume you are talking about) is G with 1/nm as a unit. It gives the probability that a particle has moved a distance r. The 1/nm is the normalization to make the values bin-size independent. Might it be that the difference in interpretation comes from if you consider normalization of the volume of sphere-shells or not? Berk > From: c...@purdue.edu > To: gmx-users@gromacs.org > Date: Tue, 4 Aug 2009 10:25:33 -0400 > Subject: [gmx-users] g_vanhove output > > Hi all, > I believe there is a mistake in g_vanhove in version 4.0.5 > The 'xvg' output file labels the y axis as G, with nm^-1 as units. > From the units, I guessed that the output was actually r^2 G, however > the initial slope is linear and not quadratic. After a few tries I > concluded that > the output is actually r*G, which is not something really useful. > I wonder if someone could look at the code and confirm this doubt in > one way or another. > > Many thank, > > Marcelo Carignano. > > PS: I couldn't find this on the list, but it has been difficult to > access the > archives lately. > ___ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php See all the ways you can stay connected to friends and family ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_vanhove output
Thanks Berk. I did look at the code, but it is not that easy to understand. My conclusion comes from this: for a diffusive regime, G(r) should be a gaussian function, with the diffusion coefficient characterizing the width. I did some tests, and I could match both curves (one from g_vanhove and the other from the diff.coef) only if I multiply the output of g_vanhove by r and normalizing again, which makes little sense to me. It would be ok to output G(r) or r^2*G(r), but to output r*G(r) seems a mistake Thanks again, Marcelo PS: I did consider the spherical integration. On Aug 4, 2009, at 10:41 AM, Berk Hess wrote: Hi, You can look at the code yourself :) I coded this and -or (which I assume you are talking about) is G with 1/nm as a unit. It gives the probability that a particle has moved a distance r. The 1/nm is the normalization to make the values bin-size independent. Might it be that the difference in interpretation comes from if you consider normalization of the volume of sphere-shells or not? Berk > From: c...@purdue.edu > To: gmx-users@gromacs.org > Date: Tue, 4 Aug 2009 10:25:33 -0400 > Subject: [gmx-users] g_vanhove output > > Hi all, > I believe there is a mistake in g_vanhove in version 4.0.5 > The 'xvg' output file labels the y axis as G, with nm^-1 as units. > From the units, I guessed that the output was actually r^2 G, however > the initial slope is linear and not quadratic. After a few tries I > concluded that > the output is actually r*G, which is not something really useful. > I wonder if someone could look at the code and confirm this doubt in > one way or another. > > Many thank, > > Marcelo Carignano. > > PS: I couldn't find this on the list, but it has been difficult to > access the > archives lately. > ___ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php See all the ways you can stay connected to friends and family ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_vanhove output
Hi, You can look at the code yourself :) I coded this and -or (which I assume you are talking about) is G with 1/nm as a unit. It gives the probability that a particle has moved a distance r. The 1/nm is the normalization to make the values bin-size independent. Might it be that the difference in interpretation comes from if you consider normalization of the volume of sphere-shells or not? Berk > From: c...@purdue.edu > To: gmx-users@gromacs.org > Date: Tue, 4 Aug 2009 10:25:33 -0400 > Subject: [gmx-users] g_vanhove output > > Hi all, > I believe there is a mistake in g_vanhove in version 4.0.5 > The 'xvg' output file labels the y axis as G, with nm^-1 as units. > From the units, I guessed that the output was actually r^2 G, however > the initial slope is linear and not quadratic. After a few tries I > concluded that > the output is actually r*G, which is not something really useful. > I wonder if someone could look at the code and confirm this doubt in > one way or another. > > Many thank, > > Marcelo Carignano. > > PS: I couldn't find this on the list, but it has been difficult to > access the > archives lately. > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_vanhove output
Hi all, I believe there is a mistake in g_vanhove in version 4.0.5 The 'xvg' output file labels the y axis as G, with nm^-1 as units. From the units, I guessed that the output was actually r^2 G, however the initial slope is linear and not quadratic. After a few tries I concluded that the output is actually r*G, which is not something really useful. I wonder if someone could look at the code and confirm this doubt in one way or another. Many thank, Marcelo Carignano. PS: I couldn't find this on the list, but it has been difficult to access the archives lately. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
