Re: [gmx-users] Re, g_rdf
On 11/1/12 12:25 PM, Ali Alizadeh wrote: Dear Justin These attachments are my rdf,g(r) profiles, http://tb18.trainbit.com/d/8692999884.jpg http://tb18.trainbit.com/d/6692999884.jpg http://tb18.trainbit.com/d/9692999884.jpg You've got an inhomogeneous system; you can't expect it to behave like a homogeneous system. For a system of pure water, convergence to 1 is expected. For a multi-layer system like this one, I don't know what the expected outcome is for the RDF. -Justin Dear All users I have a system that contains water , methane and propane in 240 k and 300 bar, My simulation box is rectangular . Water film is in middle of my box. Methane and propane is around it. My simulation box is symmetric, 1- I used g_rdf program for . My result is exotic. My g(r) in profile do not reach to ! Why 2- I test my number density profiles(from g_density) but they do not correct result because when i calculate number of my molecules by multiplying volume to average number density, i can not take the same number of my particle, Where do i mistake? -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: g_rdf: normalization issues?
Hi, If you expect a dilute homogeneous distribution and you make an rdf between a group and itself, it should go to 1-1/N. But for for instance liquid water it would go to 1, since the (N-1)/N molecules can sample the whole volume minus the volume of one molecule. Berk. Date: Thu, 8 May 2008 16:34:34 +0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Re: g_rdf: normalization issues? Thanks! Ok, so just to be clear, should I expect my RDF to go to 1 or 1-1/N at a sufficiently large range? 2008/5/8 Berk Hess <[EMAIL PROTECTED]>: Hi, The integrated rdf's never go to 1, since your box has corners which fall out of a sphere. The normalization should be ok. Some time ago the normalization was slightly different, g_rdf normalized with the number of atoms - 1, if both groups were identical. I removed this in, I think, 3.3.2. Berk. Date: Thu, 8 May 2008 15:18:47 +0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] Re: g_rdf: normalization issues? Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the molecule); still, the integrated RDF values seem to deviate from what ithey're supposed to be... 2008/5/8 Vasilii Artyukhov <[EMAIL PROTECTED]>: Hi, I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in water. What puzzles me is that sometimes in, e.g., two sequential runs, I get two RDF's with one of them having uniformly larger values than the other. Given the fact that the RDF should in principle be normalized, this seems very strange. In fact, the intergrated values of RDFs that I get seem smaller than 1*Rmax. How is this possible? Is this due to some finite box size effect or something else that I'm unaware of? Best regards, Vasilii Express yourself instantly with MSN Messenger! MSN Messenger ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: g_rdf: normalization issues?
Thanks! Ok, so just to be clear, should I expect my RDF to go to 1 or 1-1/N at a sufficiently large range? 2008/5/8 Berk Hess <[EMAIL PROTECTED]>: > Hi, > > The integrated rdf's never go to 1, since your box has corners which fall > out of a sphere. > The normalization should be ok. > Some time ago the normalization was slightly different, g_rdf normalized > with the number > of atoms - 1, if both groups were identical. I removed this in, I think, > 3.3.2. > > Berk. > > > > -- > Date: Thu, 8 May 2008 15:18:47 +0400 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Re: g_rdf: normalization issues? > > > Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the > molecule); still, the integrated RDF values seem to deviate from what > ithey're supposed to be... > > 2008/5/8 Vasilii Artyukhov <[EMAIL PROTECTED]>: > > Hi, > > I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in > water. What puzzles me is that sometimes in, e.g., two sequential runs, I > get two RDF's with one of them having *uniformly* larger values than the > other. Given the fact that the RDF should in principle be normalized, this > seems very strange. In fact, the intergrated values of RDFs that I get seem > smaller than 1*Rmax. How is this possible? Is this due to some finite box > size effect or something else that I'm unaware of? > > Best regards, Vasilii > > > > -- > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Re: g_rdf: normalization issues?
Hi, The integrated rdf's never go to 1, since your box has corners which fall out of a sphere. The normalization should be ok. Some time ago the normalization was slightly different, g_rdf normalized with the number of atoms - 1, if both groups were identical. I removed this in, I think, 3.3.2. Berk. Date: Thu, 8 May 2008 15:18:47 +0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] Re: g_rdf: normalization issues? Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the molecule); still, the integrated RDF values seem to deviate from what ithey're supposed to be... 2008/5/8 Vasilii Artyukhov <[EMAIL PROTECTED]>: Hi, I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in water. What puzzles me is that sometimes in, e.g., two sequential runs, I get two RDF's with one of them having uniformly larger values than the other. Given the fact that the RDF should in principle be normalized, this seems very strange. In fact, the intergrated values of RDFs that I get seem smaller than 1*Rmax. How is this possible? Is this due to some finite box size effect or something else that I'm unaware of? Best regards, Vasilii _ 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: g_rdf: normalization issues?
Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the molecule); still, the integrated RDF values seem to deviate from what ithey're supposed to be... 2008/5/8 Vasilii Artyukhov <[EMAIL PROTECTED]>: > Hi, > > I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in > water. What puzzles me is that sometimes in, e.g., two sequential runs, I > get two RDF's with one of them having *uniformly* larger values than the > other. Given the fact that the RDF should in principle be normalized, this > seems very strange. In fact, the intergrated values of RDFs that I get seem > smaller than 1*Rmax. How is this possible? Is this due to some finite box > size effect or something else that I'm unaware of? > > Best regards, Vasilii > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
