Re: [gmx-users] Velocity autocorrelation function
On Mon, Aug 15, 2011 at 11:16 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Using g_velacc I can calculate the velocity autocorrelation function of a group as a vector. Can I calculate the velocity autocorrelation function as a scalar? My naïve suggestion would be to take the norm of that vector. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Velocity autocorrelation function
On Thu, 2011-08-18 at 15:44 +0200, Elton Carvalho wrote: On Mon, Aug 15, 2011 at 11:16 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Using g_velacc I can calculate the velocity autocorrelation function of a group as a vector. Can I calculate the velocity autocorrelation function as a scalar? Actually I do not understand what you are pointing at. The velocity autocorrelation function is a scalar property, as it is the dot product of two vectors. Either I apply the -mol flag or not, two lines are contained in vac.xvg: time vs. c(t) However I think the description is outdated. It is claimed that for the mol flag an index group of molecule numbers is required, but if the a group of atoms is provided, it is split into the correct number of molecules. /Flo My naïve suggestion would be to take the norm of that vector. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Velocity autocorrelation function of water using g_velacc
On 2011-05-23 20.52, Justin A. Lemkul wrote: Andrew DeYoung wrote: Hi, I have run a simulation of 254 SPC/E water molecules in a cubic box of edge length 19.660 Angstrom. I have used the gromacs utility g_velacc to calculate the velocity autocorrelation function for the motion of only the oxygen atoms. When I plot the velocity autocorrelation function versus time, my result is a curve with more than one local minimum. My question is, should I expect having more than one local minimum? I am not sure that my result is reasonable. For example, the Democritus molecular dynamics website gives one example of a velocity autocorrelation function, although they do not specifically say what system (water or something else?) or what state (liquid or gas?) was used: http://www.cse.scitech.ac.uk/ccg/software/Democritus/Theory/vaf.html . Their plot shows one strong local minimum and one weaker one; both of these local minima are in the negative regime. I am new to this field, but I believe that the strong local minimum corresponds conceptually to the recoil of the atoms when they collide. If you have time, could you please look at my result at http://www.andrew.cmu.edu/user/adeyoung/velacc_may23.pdf and see if you think it is a qualitatively reasonable result? My main concern is the first local minimum, which I have labeled with an arrow on the plot. This minimum is in the _positive_ regime, which I believe (but I am not sure) cannot correspond to the recoil of atoms when they collide. In my pdf file I have displayed the parameters I have used for equilibration and dynamics. To summarize, I have used the leap frog algorithm with 2 ns equilibration in 1 fs steps, and 5 ns dynamics in 1 fs steps. For dynamics, I have saved configurations every 2 fs. Although my result from g_velacc has velocity autocorrelation frunction data from 0 to 1000 ps, the function decays rapidly to zero (as it should, I think, because the velocity rapidly decorrelates since the atoms/molecules forget their initial velocities), so I have plotted only from 0 to 1 ps. I am running Gromacs version 4.5.4. I don't know if this explains your result or not, but you do realize that if you have gen_vel = yes at the beginning of your simulation for data collection, it negates any value in previous equilibration, right? You've destroyed the ensemble you created before. You should pass the checkpoint file from the equilibration run to grompp -t and set gen_vel = no for your simulation. I'd start by doing that and seeing if it affects the result, because at this point, it may just be that you haven't properly re-equilibrated, or at the very least, the original frames are messing with the VACF calculation. -Justin Or you can just omit the first 100 ps from the analysis. There can be multiple minima, not a problem. If you integrate the VACF you should get the diffusion constant (3D), check manual and compare to g_msd. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] velocity autocorrelation function.
On 2010-06-03 08.23, #ZHAO LINA# wrote: Hi, When I looked up the manual about the autocorrelation (Chapter 8.5. Correlation functions). There is a very general (simple) descriptions. I feel I need a bit more deep-relevant references. gmx_velacc.c (g_velacc) which computes the velocity autocorrelation function, it's really hard for me to read such a nice codes. If I want to know much more about the specific formula of velocity autocorrelation functions which is being used in gromacs and how it's implemented, which way I should go? Great appreciation for any advice, Best Regards, lina This is described quite well in the textbook by Allen adn Tildesley (1987) you will find the reference in the manual. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] velocity autocorrelation function.
On 2010-06-03 08.23, #ZHAO LINA# wrote: Hi, When I looked up the manual about the autocorrelation (Chapter 8.5. Correlation functions). There is a very general (simple) descriptions. I feel I need a bit more deep-relevant references. gmx_velacc.c (g_velacc) which computes the velocity autocorrelation function, it's really hard for me to read such a nice codes. If I want to know much more about the specific formula of velocity autocorrelation functions which is being used in gromacs and how it's implemented, which way I should go? Great appreciation for any advice, Best Regards, lina This is described quite well in the textbook by Allen adn Tildesley (1987) you will find the reference in the manual. Thanks, I am reading this ebook now. Just wonder there are some latest ones. Best Regards, lina -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- -- 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
