[gmx-users] Problem with g_rdf
My understanding is the following: If you performed a simulation and then analyse it with different values for 'nrexcl' the results will differ since a different amount of interactions are excluded. It seems that the exclusion only helps for '-rdf atom' and not for '-rdf mol_com'. But the underlying simulation is the same (you got the output with a unique input), only the way you analyse the results changes... If you change the *.tpr (change 'nrexcl') and run a new simulation, you would get complete different results, i.e. the underlying simulations changes, due to the fact that you excluded some interactions. More important, the results are wrong (from a force field perspective). If you turn for a protein 'nrexcl' so high, that the intramolecular non-bonded interaction don't get calculated, the protein might unfold really fast, since there are no more hydrogen bonds etc... Think there are some special cases, where one is interested in turning of these interactions, but in most cases the resulting trajectory would be for the trash bin. Greetings Thomas Dear Thomas I have a question you and Justin, I had this problem like you, As Justin said you have to exclude all intermolecular interaction by increasing nrexcl in your topology file, I have done the step that there is in gromacs manual, My peak values decreased. But I have a question(Justin and you): When I change nrexcl in my topology file, I use grompp to create .tpr file, Then I use this .tpr file to represent rdf(with my prior results), Now, I like changing the nrexcl in topology for my new simulation, Does my result change? What is the differences between my first simulation and second simulation? On 2/19/13 3:10 PM, Thomas Schlesier wrote: > Dear all, > I have a question regarding g_rdf. > My system consits of 10 disacchardids (in the following A-B, with > A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF > (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B > > A-A and B-B is no problem. > But for A-B g_rdf determines the intermolecular contribution (which i want) AND > the intramolekular contribution (which i wanted to be excluded). > > Any (nice) ideas to solve this problem for GMX 4.0.7? > > Long way would be to calculate each intermolecular contribution individual and > average over all. Would require some scripting :( so any better solutions are > welcome. > Create a topology with a value of nrexcl sufficient to exclude all intramolecular interactions and create a .tpr file from it. Use that as input to g_rdf. -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] Problem with g_rdf
Excuseme dear Dr. Tomas, forgiveme the boldness, I'm new with this, and I dont know who to address when I have a problem. My name is Hector, and I'm tryng to install the gromacs software in my computer; I follewed all the steps in the online manual, however when I compile Gromacs with the instruction: ngmx, I receiveç the following sentence: :-) G R O M A C S (-: Glycine aRginine prOline Methionine Alanine Cystine Serine :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) ngmx (-: Option Filename Type Description -f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr InputRun input file: tpr tpb tpa -n index.ndx Input, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) --- Program ngmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737 Can not open file: topol.tpr --- "It's Calling Me to Break my Bonds, Again..." (Van der Graaf) I don't understand what to do with this, may be you can get me a hint, thank you very much and excuse me. Best regards. On Tue, 19 Feb 2013 23:04:48 +0100 Thomas Schlesier wrote: On 2/19/13 3:10 PM, Thomas Schlesier wrote: > Dear all, > I have a question regarding g_rdf. > My system consits of 10 disacchardids (in the following A-B, with > A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF > (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B > > A-A and B-B is no problem. > But for A-B g_rdf determines the intermolecular contribution (which i want) AND > the intramolekular contribution (which i wanted to be excluded). > > Any (nice) ideas to solve this problem for GMX 4.0.7? > > Long way would be to calculate each intermolecular contribution individual and > average over all. Would require some scripting :( so any better solutions are > welcome. > Create a topology with a value of nrexcl sufficient to exclude all intramolecular interactions and create a .tpr file from it. Use that as input to g_rdf. -Justin - Thanks for the suggestion. But it doesn't really fix the problem (or i don't get it). Ok what i have done (as an example only 3 molecules, A1 are all atoms of ring A of molecule 1, other stuff analogous) Index group: [ A ] A1 A2 A3 [ B ] B1 B2 B3 [ both ] A1 B1 A2 B2 A3 B3 RDF(A-A): chose two times group A RDF(B-B): chose two times group B RDF(A-B): ? If i chose group A and B i get the same result with 'nrexcel 3 or 10', i.e. mixing of intra- and intermolecluar A-B distances. If i chose 'both' two-times, i get the impression the the result is the RDF between the whole disaccharides, i.e. A1 and B1 are recognised as one molecule (AB)1 and i get the RDF between: (AB)1 - (AB)2 ; (AB)1-(AB)3 ; (AB)2-(AB)3 I tested this also with an index-file with only 1 molecule. RDF(A-B) gives the intramolecular RDF RDF(both) is zero, because the is only one molecule, center of mass distance must be zero. This also doesn't depend on using 'nrexcel 3 or 10' Did i made a mistake? Or any further ideas? Greetings Thomas -- 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 La información de este correo así como la contenida en los documentos que se adjuntan, pueden ser objeto de solicitudes de acceso a la información. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gm
Re: [gmx-users] Problem with g_rdf
On 2/19/13 5:04 PM, Thomas Schlesier wrote: On 2/19/13 3:10 PM, Thomas Schlesier wrote: > Dear all, > I have a question regarding g_rdf. > My system consits of 10 disacchardids (in the following A-B, with > A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF > (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B > > A-A and B-B is no problem. > But for A-B g_rdf determines the intermolecular contribution (which i want) AND > the intramolekular contribution (which i wanted to be excluded). > > Any (nice) ideas to solve this problem for GMX 4.0.7? > > Long way would be to calculate each intermolecular contribution individual and > average over all. Would require some scripting :( so any better solutions are > welcome. > Create a topology with a value of nrexcl sufficient to exclude all intramolecular interactions and create a .tpr file from it. Use that as input to g_rdf. -Justin - Thanks for the suggestion. But it doesn't really fix the problem (or i don't get it). Ok what i have done (as an example only 3 molecules, A1 are all atoms of ring A of molecule 1, other stuff analogous) Index group: [ A ] A1 A2 A3 [ B ] B1 B2 B3 [ both ] A1 B1 A2 B2 A3 B3 RDF(A-A): chose two times group A RDF(B-B): chose two times group B RDF(A-B): ? If i chose group A and B i get the same result with 'nrexcel 3 or 10', i.e. mixing of intra- and intermolecluar A-B distances. If i chose 'both' two-times, i get the impression the the result is the RDF between the whole disaccharides, i.e. A1 and B1 are recognised as one molecule (AB)1 and i get the RDF between: (AB)1 - (AB)2 ; (AB)1-(AB)3 ; (AB)2-(AB)3 I tested this also with an index-file with only 1 molecule. RDF(A-B) gives the intramolecular RDF RDF(both) is zero, because the is only one molecule, center of mass distance must be zero. This also doesn't depend on using 'nrexcel 3 or 10' Did i made a mistake? Or any further ideas? No, I missed a piece of information in your original post. The nrexcl approach only works with -rdf atom. I would suspect that if you want to use -rdf mol_com, you will have to have individual groups for which you want the RDF around the central group. You can analyze all the B groups around each A (and vice versa, if you need to) using the -ng flag. -Justin -- 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
[gmx-users] Problem with g_rdf
On 2/19/13 3:10 PM, Thomas Schlesier wrote: > Dear all, > I have a question regarding g_rdf. > My system consits of 10 disacchardids (in the following A-B, with > A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF > (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B > > A-A and B-B is no problem. > But for A-B g_rdf determines the intermolecular contribution (which i want) AND > the intramolekular contribution (which i wanted to be excluded). > > Any (nice) ideas to solve this problem for GMX 4.0.7? > > Long way would be to calculate each intermolecular contribution individual and > average over all. Would require some scripting :( so any better solutions are > welcome. > Create a topology with a value of nrexcl sufficient to exclude all intramolecular interactions and create a .tpr file from it. Use that as input to g_rdf. -Justin - Thanks for the suggestion. But it doesn't really fix the problem (or i don't get it). Ok what i have done (as an example only 3 molecules, A1 are all atoms of ring A of molecule 1, other stuff analogous) Index group: [ A ] A1 A2 A3 [ B ] B1 B2 B3 [ both ] A1 B1 A2 B2 A3 B3 RDF(A-A): chose two times group A RDF(B-B): chose two times group B RDF(A-B): ? If i chose group A and B i get the same result with 'nrexcel 3 or 10', i.e. mixing of intra- and intermolecluar A-B distances. If i chose 'both' two-times, i get the impression the the result is the RDF between the whole disaccharides, i.e. A1 and B1 are recognised as one molecule (AB)1 and i get the RDF between: (AB)1 - (AB)2 ; (AB)1-(AB)3 ; (AB)2-(AB)3 I tested this also with an index-file with only 1 molecule. RDF(A-B) gives the intramolecular RDF RDF(both) is zero, because the is only one molecule, center of mass distance must be zero. This also doesn't depend on using 'nrexcel 3 or 10' Did i made a mistake? Or any further ideas? Greetings Thomas -- 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] Problem with g_rdf
On 2/19/13 3:10 PM, Thomas Schlesier wrote: Dear all, I have a question regarding g_rdf. My system consits of 10 disacchardids (in the following A-B, with A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B A-A and B-B is no problem. But for A-B g_rdf determines the intermolecular contribution (which i want) AND the intramolekular contribution (which i wanted to be excluded). Any (nice) ideas to solve this problem for GMX 4.0.7? Long way would be to calculate each intermolecular contribution individual and average over all. Would require some scripting :( so any better solutions are welcome. Create a topology with a value of nrexcl sufficient to exclude all intramolecular interactions and create a .tpr file from it. Use that as input to g_rdf. -Justin -- 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
[gmx-users] Problem with g_rdf
Dear all, I have a question regarding g_rdf. My system consits of 10 disacchardids (in the following A-B, with A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B A-A and B-B is no problem. But for A-B g_rdf determines the intermolecular contribution (which i want) AND the intramolekular contribution (which i wanted to be excluded). Any (nice) ideas to solve this problem for GMX 4.0.7? Long way would be to calculate each intermolecular contribution individual and average over all. Would require some scripting :( so any better solutions are welcome. Greetings Thomas -- 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
[gmx-users] Problem with g_rdf plot
Hi everyone, I ran a water simulation and I tried to calculate radial distribution function OO but I get strange peaks from r =1.5nm onwards. I have 8 atoms in a box of 9.5. I post the graph as an attached file. Please does anyone have an idea of what might be going on? Thanks, Carla rdf_Ow-Ow-15to17ns.dat Description: MOPAC data rdf_Ow-Ow-15to17ns.xvg Description: Binary data -- 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
[gmx-users] Problem with g_rdf /option com
Hi, I want to get the radial distribution of my system which is composed of a box of capped alanine residues (CAR). In this respect, I used g_rdf command with -com option. I chose one of the CAR s as the first, and the others as the second group. In manual, for -com option, it is written that the center of mass is chosen only for the first group. Does it mean that for the second group all the atoms are taken into consideration? If so, is there any option for taking the center of masses of molecules in the second group? Thanks Ozge. ___ 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] problem with g_rdf
> What is the problem? Couple of things I would look at first, open the file generated by g_rdf using a text editor and look at the actual values in there. Then ensure that what ever you are plotting the data with, is using the correct data / columns presented in the data file. If you still see the same issue after that, then you need to start looking at the command line used, and the various files used on it, ensure they are consistent with each other etc. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] problem with g_rdf
OZGE ENGIN wrote: Hi, First of all, I wish, everything is o.k for everybody :) I have a question about the g_rdf command. I read the mailing list but I could not find any problem simiIar to mine. I want to calculate the radial distribution function of my system which consists of tripeptide and water molecules. In this respect, I select two groups: the peptide as the first and the water molecules as the second.Then I plotted the given rdf.xvg file, and what I saw was not an expected one. The distribution of particles increased with respect to increasing distance. I could not get the values of g(r ) on the y axis. You shall use xmgrace -nxy to view g_rdf's output. The distribution did not show the first and the second peaks that correspond to the first and the second hydration shells, respectively. Sorry. You but not me shall answer this. What is the problem? Thanks in advance Ozge Engin ___ 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
[gmx-users] problem with g_rdf
Hi, First of all, I wish, everything is o.k for everybody :) I have a question about the g_rdf command. I read the mailing list but I could not find any problem simiIar to mine. I want to calculate the radial distribution function of my system which consists of tripeptide and water molecules. In this respect, I select two groups: the peptide as the first and the water molecules as the second.Then I plotted the given rdf.xvg file, and what I saw was not an expected one. The distribution of particles increased with respect to increasing distance. I could not get the values of g(r ) on the y axis.The distribution did not show the first and the second peaks that correspond to the first and the second hydration shells, respectively. What is the problem? Thanks in advance Ozge Engin ___ 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
