Re: [gmx-users] RF and TI
But my system is rigid benzene molecule, and all intramolecular interactions are absent. The RF modifies a short-range electrostatic potential. Is it correct for both decoupling scheme and manual method? Where is the difference? And what about additive constant (named Crf in the manual, formula 4.14), is it also included in the dH/dl? Alexey 2009/12/4 Berk Hess g...@hotmail.com: Hi, Yes, RF in the couple scheme is correct. The manual calculation you did is incorrect. In the decoupled state the intra-molecular interactions of the decoupled molecule should not be RF, but plain Coulomb. The couple option does this correctly. Berk Date: Fri, 4 Dec 2009 15:52:58 +0300 From: ale.odino...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] RF and TI Dear gmx users, I calculated the hydration free energy of benzene molecule two times. First time I used a decoupling method implemented in GROMACS. Second time I performed thermodynamical integration between different topologies of the benzene molecule: non-interacting with media and normal one. All intramolecular interactions were turned off. The results were different: decoupling method gave energies about 2.8 kcal/mol higher. I investigated the problem and found that the difference of the dH/dl values was due to the Reaction-field term. When I switched electrostatic to the simple cut-off scheme, decoupling method gave almost the same result, while for dual topology method the result increased on 2-3 kcal/mol. Is the RF method consistent with free energy calculations? Can it be treated within the frames of decoupling scheme? Thanks, Alexey -- 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 New Windows 7: Find the right PC for you. Learn more. -- gmx-users mailing list gmx-us...@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
[gmx-users] Problems
When defining the box dimention then how do I know about the distance of protein from the box wall? Which should be greater than half of the Cut-Off (1.4nm) (according to some tutorial). Then what are longest cutoff which must be shorter than half the shortest box vector to satisfy the minimum image convention. I am asking because I have run gromacs from default parameter of some other tutorial. I have used 0.75 value for -d when using editconf. -- Pawan -- 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] Problems
pawan raghav wrote: When defining the box dimention then how do I know about the distance of protein from the box wall? Which should be greater than half of the You know because you specify it with editconf -d :) Cut-Off (1.4nm) (according to some tutorial). This solute-wall distance is not the one that is related to the cutoff (directly). It is the size of the resulting box that is of concern. Then what are longest cutoff which must be shorter than half the shortest box vector to satisfy the minimum image convention. I am asking because I have run gromacs from default parameter of some other tutorial. I have used 0.75 value for -d when using editconf. The cutoffs are what you specify in the .mdp file (rcoulomb, rvdw) - these must be less than 1/2 the shortest box vector. As for how you design the box, that will be dependent upon the size of the solute. For most globular proteins, the choice when running editconf -d is not terribly sensitive, although one usually sees a value of ~1.0 nm used in the literature. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] Re: gmx-users Digest, Vol 68, Issue 35
Stefan Hoorman wrote: Stefan Hoorman wrote: How can I calculate the angle between a helix inserted in a membrane and the axis perpendicular to the surface of the membrane. I have tried using g_helixorient, but the graphs all come as a straight line in zero. See -z in g_sgangle -h Mark Thank you for the tip, but again I faced a problem. I could only analyse using g_sgangle with an index group containing 3 atoms. Then the problem is, since my helix not only tilts, but also it bends a little back and forth, the angle between it and the z axis will vary greatly depending on which three atoms I choose. I imagined that by choosing three alpha carbon atoms every four residues would give me a good outcome, but it turns out that the angle changes a lot, and I am guessing it is because of this bending movement. When I say changes a lot I mean; it starts at 0º and gets up to 50º, which i imagine to be a little bit too much. Would there be a better way to calculate this? g_principal will calculate the axes of inertia, from which you can calculate the angle with the Z-axis. Mark Ok, thank you for the info, but now I got a little bit confused. What exactly does the info from axis1.dat, axis2.dat, axis3.dat and moi.dat mean? And how would I use this info to calculate the helix tilt. I know the general meaning of principal axes of inertia, but I could not find any information more specific to this type of caltulation I need to do. If you could give any reference or any other type of information a little bit more specific I would be very greatful. I mean, if it is not too much to ask. Thank you Stef. -- 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] Reducing Standard Error output
Even though I can sucessfully run this when I remove the verbose flag, it causes another problem. We keep trac of the progress of indivual simulations using a code modfication in sim_util.c 124: f = fopen(progress.txt, w); 125- if (!f) return; 126- fprintf(f, %g, (step - ir-init_step) / (float) ir-nsteps); 127- fclose(f); Apparently this code is only used if the app is in verbose mode. So I guess we have two choices: 1) either find the cause of the lincs warnings 2) modify the code so it reports progress regardless of verbose flag On Thu, Dec 3, 2009 at 7:39 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: yes the environment I was running in was the boinc wrapper and its supposed to somehow return the standard error output. It probably got overloaded. It is curious why I only had the problem on windows 64 but I'm not going to worry about it. On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. mdrun -v will have no effect on correct completion, unless the use of -v is causing some I/O buffer external to GROMACS to over-run. I suspect your observation indicates you were comparing apples and oranges. Mark -- gmx-users mailing list gmx-us...@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 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] intramolecular LJ and Coulomb interactions
Vitaly V. Chaban wrote: Hi, Is there a way to output only intramolecular interaction (LJ and Coulomb but not bond, angle, etc) energies (with a respect of exclusions, of course). It seems LJ-(SR) and Coulomb-(SR) terms in g_energy include all interaction, both inter- and intramolecular ones. Use energygrps in the .mdp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] Re: intramolecular LJ and Coulomb interactions
On Sat, Dec 5, 2009 at 10:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: Vitaly V. Chaban wrote: Hi, Is there a way to output only intramolecular interaction (LJ and Coulomb but not bond, angle, etc) energies (with a respect of exclusions, of course). It seems LJ-(SR) and Coulomb-(SR) terms in g_energy include all interaction, both inter- and intramolecular ones. Use energygrps in the .mdp file. -Justin This will evidently work with one molecule. One group (MOL) contains the atoms of one molecule and then one calculates MOL-MOL interactions with g_energy. Is there no automatic way to perform such calculations with all molecules in the system? Maybe it's not principal as the single molecule intramolecular energies should be very close... -- 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] Re: intramolecular LJ and Coulomb interactions
Vitaly V. Chaban wrote: On Sat, Dec 5, 2009 at 10:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: Vitaly V. Chaban wrote: Hi, Is there a way to output only intramolecular interaction (LJ and Coulomb but not bond, angle, etc) energies (with a respect of exclusions, of course). It seems LJ-(SR) and Coulomb-(SR) terms in g_energy include all interaction, both inter- and intramolecular ones. Use energygrps in the .mdp file. -Justin This will evidently work with one molecule. One group (MOL) contains the atoms of one molecule and then one calculates MOL-MOL interactions with g_energy. Is there no automatic way to perform such calculations with all molecules in the system? Maybe it's not principal as the single molecule intramolecular energies should be very close... To get the intermolecular energies decomposed among many species, you would still use energygrps, but if you have many species, the .edr file can potentially get very large since the intermolecular interactions are then calculated for each pair of energygrps, unless you use energygrp_excl. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] Reducing Standard Error output
Jack Shultz wrote: Even though I can sucessfully run this when I remove the verbose flag, it causes another problem. We keep trac of the progress of indivual simulations using a code modfication in sim_util.c 124: f = fopen(progress.txt, w); 125- if (!f) return; 126- fprintf(f, %g, (step - ir-init_step) / (float) ir-nsteps); 127- fclose(f); Apparently this code is only used if the app is in verbose mode. So I guess we have two choices: 1) either find the cause of the lincs warnings That is always necessary if you don't want an expensive random number generator. Your simulation system is ill conditioned, and the lincs warnings will exist and be reported in at least the .log file regardless of the verbosity. 2) modify the code so it reports progress regardless of verbose flag Sure, but that's independent of the former. You should consider other modifications too - opening and closing a file every integration step might be prohibitively expensive. Since from previous threads you're monitoring this progress file with some other process to report to the user, you should consider more efficient means of such communication, such as an inter-process socket. Mark On Thu, Dec 3, 2009 at 7:39 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: yes the environment I was running in was the boinc wrapper and its supposed to somehow return the standard error output. It probably got overloaded. It is curious why I only had the problem on windows 64 but I'm not going to worry about it. On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. mdrun -v will have no effect on correct completion, unless the use of -v is causing some I/O buffer external to GROMACS to over-run. I suspect your observation indicates you were comparing apples and oranges. Mark -- 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 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Re: gmx-users Digest, Vol 68, Issue 35
Stefan Hoorman wrote: Stefan Hoorman wrote: Stefan Hoorman wrote: How can I calculate the angle between a helix inserted in a membrane and the axis perpendicular to the surface of the membrane. I have tried using g_helixorient, but the graphs all come as a straight line in zero. See -z in g_sgangle -h Mark Thank you for the tip, but again I faced a problem. I could only analyse using g_sgangle with an index group containing 3 atoms. Then the problem is, since my helix not only tilts, but also it bends a little back and forth, the angle between it and the z axis will vary greatly depending on which three atoms I choose. I imagined that by choosing three alpha carbon atoms every four residues would give me a good outcome, but it turns out that the angle changes a lot, and I am guessing it is because of this bending movement. When I say changes a lot I mean; it starts at 0º and gets up to 50º, which i imagine to be a little bit too much. Would there be a better way to calculate this? g_principal will calculate the axes of inertia, from which you can calculate the angle with the Z-axis. Mark Ok, thank you for the info, but now I got a little bit confused. What exactly does the info from axis1.dat, axis2.dat, axis3.dat and moi.dat mean? I don't know, I've never seen them. I'd be expecting three numbers in each to indicate a vector parallel to the axis. And how would I use this info to calculate the helix tilt. I know the general meaning of principal axes of inertia, but I could not find any information more specific to this type of caltulation I need to do. If you could give any reference or any other type of information a little bit more specific I would be very greatful. I mean, if it is not too much to ask. This is standard geometry - dot-products of vectors are related to the cosine of the angle between them. Check wikipedia. Mark -- 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] Questions about hydrogen bond lifetime
Hi, dear all (especially for David): When reading the paper Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media and its supplementary material and the code gmx_hbond.c for the analysis of hydrogen bond, I got questions: 1. When calculating the autocorrelation function of the interrupted lifetime using -ac option, is the error of the calculation given by Chi^2 in the output? 2. As can be seen from the supplementary material of the paper, the forward and backward rate k and k' are dependent on the temperature, but from the code, I can not identify the link between temp and k since temp is only used in calc_dg(), which means temp and k are not related. Am I right? Thank you. Jian -- 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
