[gmx-users] free energy
Dear Kieu Thu Thanks for your comment about free energy. Unfortunately, I could not send a email to Paissoni Cristina in the Gromacs Forum. Could you give me email address of Paissoni Cristina? Finding a tool for calculation MM/PBSA with Gromacs is very vital for me. Best Regards Kiana -- 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] free energy
Dear GMX Users I am using parmbsc0 force field to study DNA-ligand interaction but my problem is free energy calculation (MMPBSA) for this interaction. How can I calculate free energy using MMPBSA approach? Thank you very much for your time and consideration. Best Regards Kiana -- 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] free energy
On 11/5/13 3:45 AM, kiana moghaddam wrote: Dear GMX Users I am using parmbsc0 force field to study DNA-ligand interaction but my problem is free energy calculation (MMPBSA) for this interaction. How can I calculate free energy using MMPBSA approach? Thank you very much for your time and consideration. An identical question was asked on the list last week, including responses about external software that will do these calculations. Gromacs does not do MM/PBSA, but other programs will. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] free energy
Dear Kiana, You can contact with Paissoni Cristina (email: paissoni.crist...@hsr.it) to get tool using MM/PBSA with GROMACS. Hope it help :) Cheers, Kieu Thu On Tue, Nov 5, 2013 at 7:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/5/13 3:45 AM, kiana moghaddam wrote: Dear GMX Users I am using parmbsc0 force field to study DNA-ligand interaction but my problem is free energy calculation (MMPBSA) for this interaction. How can I calculate free energy using MMPBSA approach? Thank you very much for your time and consideration. An identical question was asked on the list last week, including responses about external software that will do these calculations. Gromacs does not do MM/PBSA, but other programs will. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] Free energy of solvation of large molecule
Hi, I'm trying to calculate the free energy of solvation of a relatively large polymer molecule (161 atoms). I went through the free energy tutorial published on J. Lemkul's web page but when trying to apply the same approach to my case, the simulations typically fail. The files for one such case are here: https://www.dropbox.com/s/z5z3ip767dgwloh/coul0.0.tar.gz I looked all over the internet to find a similar use case but most people seem to have studied small organic molecules, which means computing the solvation free energy for my molecule is far from trivial. I understand I'll have to do simulations at many lambda points for rather long periods of time but how to run them in a stable way? Thanks in advance, Jernej -- 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] Free Energy Ion Pair Decoupling
Dear Gromacs users, -- 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
Aw: [gmx-users] Free Energy Simulations in Parallel
Play with the domain decomposition, lincs itr/order, -ntomp and -ntmpi, etc... I was able to get a 4 day simulation which often gave that error to speed up to 12 hours on 24 CPU/3 nodes/144 cores but it took 2 days of submitting, checking speed, and killing jobs to try another grid routine. My problem related to this is it wont go any faster (more nodes, cpus or cores and starts to hit limits where there are only 100 atoms in a unit cell) if anyone knows a way to make it go faster. Sincerely, Stephan Watkins Gesendet:Freitag, 26. Juli 2013 um 22:13 Uhr Von:Quintin Sheridan qsher...@nd.edu An:gmx-users@gromacs.org gmx-users@gromacs.org Betreff:[gmx-users] Free Energy Simulations in Parallel Dear Gromacs Users, Is it possible to run free energy calculations in parallel using mpirun? If not, what is the fastest way to run free energy calculations. I am trying to us the Bennets Accepetance Ratio (g_bar) to get the free energy of solvation for an ionic liquid based on the tutorial by Justin Lemkul. I hav tried to decouple an ion pair as well as individual ions. In either case the simulations run locally but when I try to run them in parrallel I get the error: Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 2.26125 nm Thank You Quintin Sheridan -- 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/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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: Aw: [gmx-users] Free Energy Simulations in Parallel
On 7/27/13 7:02 AM, lloyd riggs wrote: Play with the domain decomposition, lincs itr/order, -ntomp and -ntmpi, etc... I was able to get a 4 day simulation which often gave that error to speed up to 12 hours on 24 CPU/3 nodes/144 cores but it took 2 days of submitting, checking speed, and killing jobs to try another grid routine. My problem related to this is it wont go any faster (more nodes, cpu's or cores and starts to hit limits where there are only 100 atoms in a unit cell) if anyone knows a way to make it go faster. In the context of free energy simulations (and the original post on this topic), the limiting factor is generally the use of couple_intramol. If set to no, as is fairly common, exclusions are generated that then limit the number of DD cells that can be used. More detail on this specific topic can be found in the list archive. -Justin Sincerely, Stephan Watkins *Gesendet:* Freitag, 26. Juli 2013 um 22:13 Uhr *Von:* Quintin Sheridan qsher...@nd.edu *An:* gmx-users@gromacs.org gmx-users@gromacs.org *Betreff:* [gmx-users] Free Energy Simulations in Parallel Dear Gromacs Users, Is it possible to run free energy calculations in parallel using mpirun? If not, what is the fastest way to run free energy calculations. I am trying to us the Bennet's Accepetance Ratio (g_bar) to get the free energy of solvation for an ionic liquid based on the tutorial by Justin Lemkul. I hav tried to decouple an ion pair as well as individual ions. In either case the simulations run locally but when I try to run them in parrallel I get the error: Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 2.26125 nm Thank You Quintin Sheridan -- 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/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 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Free Energy Calculations in Parallel
Dear Gromacs Users, Is it possible to run free energy calculations in parallel using mpirun? If not I am wondering what the fastest way to run a free energy calculation is. I am basing my free energy calculation on the tutorial by Justin Lemkul found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html I am trying to use the Bennet Acceptance Ration method (g_bar) to get the free energy of solvation for an ionic liquid. I have tried decoupling an ion pair from the system as well as individual ions. These simulations will run locally but when I try to run them in parallel I get the error: Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 2.26125 nm Thank you Quintin Sheridan -- 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] Free Energy Simulations in Parallel
Dear Gromacs Users, Is it possible to run free energy calculations in parallel using mpirun? If not, what is the fastest way to run free energy calculations. I am trying to us the Bennet's Accepetance Ratio (g_bar) to get the free energy of solvation for an ionic liquid based on the tutorial by Justin Lemkul. I hav tried to decouple an ion pair as well as individual ions. In either case the simulations run locally but when I try to run them in parrallel I get the error: Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 2.26125 nm Thank You Quintin Sheridan -- 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] Free Energy Calculations in Parallel
On 7/26/13 4:06 PM, Quintin Sheridan wrote: Dear Gromacs Users, Is it possible to run free energy calculations in parallel using mpirun? If Yes, the free energy code is parallelized, either via MPI or threads. not I am wondering what the fastest way to run a free energy calculation is. I am basing my free energy calculation on the tutorial by Justin Lemkul found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html I am trying to use the Bennet Acceptance Ration method (g_bar) to get the free energy of solvation for an ionic liquid. I have tried decoupling an ion pair from the system as well as individual ions. These simulations will run locally but when I try to run them in parallel I get the error: Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 2.26125 nm Consult http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm. This topic is discussed frequently, particularly in the context of free energy simulations, because there are unique factors that come into play in terms of the DD algorithm. Search the archive and you will surely find the detailed explanations. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2
Hi gmx-users, I almost reproduced free energy calculations of methane in water on Justin's website. First of all, I am able to follow the workflow of computing solvation free energy for several times with Gromacs version 4.5.7 and version 4.6.2 installed in two identical Linux boxes. However. the output results of GMX ver 4.5.7 and ver 4.6.2 show different values of dG ## GMX Ver. 4.5.7: lambda 0.000 - 0.050, DG 0.05 +/- 0.00 lambda 0.050 - 0.100, DG 0.01 +/- 0.00 lambda 0.100 - 0.150, DG -0.03 +/- 0.01 lambda 0.150 - 0.200, DG -0.08 +/- 0.00 lambda 0.200 - 0.250, DG -0.15 +/- 0.00 lambda 0.250 - 0.300, DG -0.21 +/- 0.01 lambda 0.300 - 0.350, DG -0.28 +/- 0.00 lambda 0.350 - 0.400, DG -0.38 +/- 0.00 lambda 0.400 - 0.450, DG -0.50 +/- 0.01 lambda 0.450 - 0.500, DG -0.66 +/- 0.01 lambda 0.500 - 0.550, DG -0.90 +/- 0.01 lambda 0.550 - 0.600, DG -1.21 +/- 0.01 lambda 0.600 - 0.650, DG -1.37 +/- 0.01 lambda 0.650 - 0.700, DG -1.25 +/- 0.01 lambda 0.700 - 0.750, DG -0.96 +/- 0.00 lambda 0.750 - 0.800, DG -0.62 +/- 0.00 lambda 0.800 - 0.850, DG -0.31 +/- 0.00 lambda 0.850 - 0.900, DG -0.03 +/- 0.00 lambda 0.900 - 0.950, DG 0.20 +/- 0.00 lambda 0.950 - 1.000, DG 0.38 +/- 0.00 total 0.000 - 1.000, DG -8.31 +/- 0.04 ## GMX ver. 4.6.2 ver point 0.000 - 0.050, DG 0.00 +/- 0.00 point 0.050 - 0.100, DG -0.03 +/- 0.00 point 0.100 - 0.150, DG -0.08 +/- 0.00 point 0.150 - 0.200, DG -0.14 +/- 0.00 point 0.200 - 0.250, DG -0.20 +/- 0.00 point 0.250 - 0.300, DG -0.27 +/- 0.00 point 0.300 - 0.350, DG -0.34 +/- 0.00 point 0.350 - 0.400, DG -0.43 +/- 0.01 point 0.400 - 0.450, DG -0.54 +/- 0.01 point 0.450 - 0.500, DG -0.71 +/- 0.01 point 0.500 - 0.550, DG -0.94 +/- 0.01 point 0.550 - 0.600, DG -1.24 +/- 0.02 point 0.600 - 0.650, DG -1.39 +/- 0.02 point 0.650 - 0.700, DG -1.28 +/- 0.01 point 0.700 - 0.750, DG -1.00 +/- 0.00 point 0.750 - 0.800, DG -0.67 +/- 0.00 point 0.800 - 0.850, DG -0.36 +/- 0.00 point 0.850 - 0.900, DG -0.09 +/- 0.00 point 0.900 - 0.950, DG 0.14 +/- 0.00 point 0.950 - 1.000, DG 0.33 +/- 0.00 total 0.000 - 1.000, DG -9.23 +/- 0.03 ## The value of DG (= -9.23 kJ mol -1) by GMX ver 4.6.2 is very close to that by Justin or Shirts et.al of 2.24 kcal mol-1 (~ -9.36 kJ mol -1), while that of GMX ver 4.5.7 ( =-8.31 kJ mol-1) is far away. I wonder if someone has similar experience to explain the inconsistency between the outputs from ver 4.5.7 (~-8.31 kJmol-1) and ver 4.6.2 (-9.23 kJmol-1 ), despite the values of dG computed by others. Second, the reason why I almost reproduced dG but not completely is because I removed the step of L- BFGS minimization. I was not able to pass this step for both GMX versions. Here shows the warning. Fatal error: The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent). L-BFGS mdp file can be found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_l-bfgs.mdp Again, I appreciate advice or a hint. Thanks, Dwey -- 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] free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2
On 6/21/13 11:07 AM, Dwey wrote: Hi gmx-users, I almost reproduced free energy calculations of methane in water on Justin's website. First of all, I am able to follow the workflow of computing solvation free energy for several times with Gromacs version 4.5.7 and version 4.6.2 installed in two identical Linux boxes. However. the output results of GMX ver 4.5.7 and ver 4.6.2 show different values of dG ## GMX Ver. 4.5.7: lambda 0.000 - 0.050, DG 0.05 +/- 0.00 lambda 0.050 - 0.100, DG 0.01 +/- 0.00 lambda 0.100 - 0.150, DG -0.03 +/- 0.01 lambda 0.150 - 0.200, DG -0.08 +/- 0.00 lambda 0.200 - 0.250, DG -0.15 +/- 0.00 lambda 0.250 - 0.300, DG -0.21 +/- 0.01 lambda 0.300 - 0.350, DG -0.28 +/- 0.00 lambda 0.350 - 0.400, DG -0.38 +/- 0.00 lambda 0.400 - 0.450, DG -0.50 +/- 0.01 lambda 0.450 - 0.500, DG -0.66 +/- 0.01 lambda 0.500 - 0.550, DG -0.90 +/- 0.01 lambda 0.550 - 0.600, DG -1.21 +/- 0.01 lambda 0.600 - 0.650, DG -1.37 +/- 0.01 lambda 0.650 - 0.700, DG -1.25 +/- 0.01 lambda 0.700 - 0.750, DG -0.96 +/- 0.00 lambda 0.750 - 0.800, DG -0.62 +/- 0.00 lambda 0.800 - 0.850, DG -0.31 +/- 0.00 lambda 0.850 - 0.900, DG -0.03 +/- 0.00 lambda 0.900 - 0.950, DG 0.20 +/- 0.00 lambda 0.950 - 1.000, DG 0.38 +/- 0.00 total 0.000 - 1.000, DG -8.31 +/- 0.04 ## GMX ver. 4.6.2 ver point 0.000 - 0.050, DG 0.00 +/- 0.00 point 0.050 - 0.100, DG -0.03 +/- 0.00 point 0.100 - 0.150, DG -0.08 +/- 0.00 point 0.150 - 0.200, DG -0.14 +/- 0.00 point 0.200 - 0.250, DG -0.20 +/- 0.00 point 0.250 - 0.300, DG -0.27 +/- 0.00 point 0.300 - 0.350, DG -0.34 +/- 0.00 point 0.350 - 0.400, DG -0.43 +/- 0.01 point 0.400 - 0.450, DG -0.54 +/- 0.01 point 0.450 - 0.500, DG -0.71 +/- 0.01 point 0.500 - 0.550, DG -0.94 +/- 0.01 point 0.550 - 0.600, DG -1.24 +/- 0.02 point 0.600 - 0.650, DG -1.39 +/- 0.02 point 0.650 - 0.700, DG -1.28 +/- 0.01 point 0.700 - 0.750, DG -1.00 +/- 0.00 point 0.750 - 0.800, DG -0.67 +/- 0.00 point 0.800 - 0.850, DG -0.36 +/- 0.00 point 0.850 - 0.900, DG -0.09 +/- 0.00 point 0.900 - 0.950, DG 0.14 +/- 0.00 point 0.950 - 1.000, DG 0.33 +/- 0.00 total 0.000 - 1.000, DG -9.23 +/- 0.03 ## The value of DG (= -9.23 kJ mol -1) by GMX ver 4.6.2 is very close to that by Justin or Shirts et.al of 2.24 kcal mol-1 (~ -9.36 kJ mol -1), while that of GMX ver 4.5.7 ( =-8.31 kJ mol-1) is far away. I wonder if someone has similar experience to explain the inconsistency between the outputs from ver 4.5.7 (~-8.31 kJmol-1) and ver 4.6.2 (-9.23 kJmol-1 ), despite the values of dG computed by others. I can't explain the difference you are seeing, but I know the results have been reproduced with versions 4.5.3 and 4.5.5. It is good to know that the latest version (4.6.2) is working as expected, but it might be useful to figure out what's up with 4.5.7. Please let me know if you can reproduce the right result with 4.5.5. Second, the reason why I almost reproduced dG but not completely is because I removed the step of L- BFGS minimization. I was not able to pass this step for both GMX versions. Here shows the warning. Fatal error: The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent). L-BFGS mdp file can be found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_l-bfgs.mdp Add define = -DFLEXIBLE to the .mdp file. Water molecules are constrained via SETTLE, so that causes issues with L-BFGS. When I designed the tutorial, grompp did not do that check, so it was ignoring those constraints and silently moving past it. I will fix the .mdp file. Thanks for bringing that to my attention. -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] Free energy calculation: merge the topology of 2 molecules
Hi all, I'm trying to set-up a free energy calculation where a molecule has +2 charge in it's native state (state A) and no charge in the mutant (state B). Since the molecule has net +2 charge, I have to add counter-ions to neutralize the system in state A. But in order to transform it to state B and still maintain a neutral system, the counter-ions have to be transformed too. I tried only transforming only the target molecule not the ions but the simulation crashes very quickly. I searched the gmx-users archives and found some suggestion about merging the topology definition of ions into that of the molecule under one [moleculetype] section. I tried that but mdrun warned me with tons of inconsistent shift: There were 2 inconsistent shifts. Check your topology There were 18 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology There were 12 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology ... and the simulation can't be run in parallel because mdrun would just quick and complain about not being able to do domain decomposition: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 29.6188 nm I guess the issue is Gromacs thinks those counter-ions belongs chemically to the target molecule although they are actually not in close proximity in space, which mess up the DD. partition. I wonder if there's a way to get around that. Thanks, Dejun -- 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
Aw: [gmx-users] Free energy calculation: merge the topology of 2 molecules
Ive had 2 problems like this. 1 was solved by doing all eq to a good degree first in one thread, then the domain decomposition worked in 8 or 16...the secound I had to break down the charge groups in the .itp (cg) into smaller charge groups and it worked, there might be better suggestions though. Stephan Gesendet:Donnerstag, 30. Mai 2013 um 20:48 Uhr Von:Dejun Lin dejun@gmail.com An:gmx-users@gromacs.org Betreff:[gmx-users] Free energy calculation: merge the topology of 2 molecules Hi all, Im trying to set-up a free energy calculation where a molecule has +2 charge in its native state (state A) and no charge in the mutant (state B). Since the molecule has net +2 charge, I have to add counter-ions to neutralize the system in state A. But in order to transform it to state B and still maintain a neutral system, the counter-ions have to be transformed too. I tried only transforming only the target molecule not the ions but the simulation crashes very quickly. I searched the gmx-users archives and found some suggestion about merging the topology definition of ions into that of the molecule under one [moleculetype] section. I tried that but mdrun warned me with tons of inconsistent shift: There were 2 inconsistent shifts. Check your topology There were 18 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology There were 12 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology ... and the simulation cant be run in parallel because mdrun would just quick and complain about not being able to do domain decomposition: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 29.6188 nm I guess the issue is Gromacs thinks those counter-ions belongs chemically to the target molecule although they are actually not in close proximity in space, which mess up the DD. partition. I wonder if theres a way to get around that. Thanks, Dejun -- 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/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Free energy calculation: merge the topology of 2 molecules
Thanks for your reply, Stephan. Did the molecule you worked with have any atoms that are isolated (non-bonded) to the others? Was the equilibration run in your 1st case just a way to recruit those isolated atoms to the others in the same molecule? I suspect I might need to add artificial bond to connect the counter-ions to the target molecule. In the 2nd case you mentioned, I'm not sure why it would work for you but not me because I essentially have every atoms in their single charge groups. Thanks, Dejun 2013/5/30 lloyd riggs lloyd.ri...@gmx.ch I've had 2 problems like this. 1 was solved by doing all eq to a good degree first in one thread, then the domain decomposition worked in 8 or 16...the secound I had to break down the charge groups in the .itp (cg) into smaller charge groups and it worked, there might be better suggestions though. Stephan *Gesendet:* Donnerstag, 30. Mai 2013 um 20:48 Uhr *Von:* Dejun Lin dejun@gmail.com *An:* gmx-users@gromacs.org *Betreff:* [gmx-users] Free energy calculation: merge the topology of 2 molecules Hi all, I'm trying to set-up a free energy calculation where a molecule has +2 charge in it's native state (state A) and no charge in the mutant (state B). Since the molecule has net +2 charge, I have to add counter-ions to neutralize the system in state A. But in order to transform it to state B and still maintain a neutral system, the counter-ions have to be transformed too. I tried only transforming only the target molecule not the ions but the simulation crashes very quickly. I searched the gmx-users archives and found some suggestion about merging the topology definition of ions into that of the molecule under one [moleculetype] section. I tried that but mdrun warned me with tons of inconsistent shift: There were 2 inconsistent shifts. Check your topology There were 18 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology There were 12 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology ... and the simulation can't be run in parallel because mdrun would just quick and complain about not being able to do domain decomposition: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 29.6188 nm I guess the issue is Gromacs thinks those counter-ions belongs chemically to the target molecule although they are actually not in close proximity in space, which mess up the DD. partition. I wonder if there's a way to get around that. Thanks, Dejun -- 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/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 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 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] Free energy of solvation's .mdp of peptide
Hi, if I want to calculate the free energy of solvation of peptide, because both van der Waals and Coulombic interactions are important for peptide so I set couple-lambda0 = none couple-lambda1 = vdw-q is it right? or it's better to choose wo-stage approach to do this work: van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype= peptide couple-intramol = no couple-lambda0= none; non-interacting dummy in state A couple-lambda1= vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype= peptide couple-intramol = no couple-lambda0= vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-energy-of-solvation-s-mdp-of-peptide-tp5008445.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] free energy of system
Dear all, I'm interested in calculating the Gibbs free energy of some systems. I have several questions in this regard: 1- The g_energy command gives some values in kJ/mol for total energy and enthalpy. Does the reported total energy include entropy effects? (The calculated total energy and enthalpy were not equal for the systems I had simulated.) Is the unit really kJ/mol? 2- Is it possible to perform md simulation as usual (like in the drug-enzyme tutorial) and run the g_bar command to get the dG results? 3- How can I get the md_$LAMBDA.mdp file? Or which lines should be added to the common md.mdp files? Best regards, Sarah Keshavarz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] free energy of system
On 4/25/13 12:02 PM, sarah k wrote: Dear all, I'm interested in calculating the Gibbs free energy of some systems. I have several questions in this regard: 1- The g_energy command gives some values in kJ/mol for total energy and enthalpy. Does the reported total energy include entropy effects? Not likely. (The calculated total energy and enthalpy were not equal for the systems I had simulated.) Is the unit really kJ/mol? Total energy and enthalpy should not necessarily be equal. Total energy is just the sum of potential and kinetic energy. The unit of kJ/mol is actually kJ per mole of equivalent systems. 2- Is it possible to perform md simulation as usual (like in the drug-enzyme tutorial) and run the g_bar command to get the dG results? That depends on your definition of as usual and what you expect as a result. You can decouple a ligand from a binding site, but that only gives you part of the information you need to calculate, for instance, the actual free energy of binding. 3- How can I get the md_$LAMBDA.mdp file? Or which lines should be added to the common md.mdp files? Given the nomenclature, I assume you are referring to files in my free energy tutorial, which are created by scripts. All the answers to this question are in my tutorial. -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
Re: [gmx-users] Free Energy Calculations in Gromacs
Thank you Professor Shirts. So now my protein itp file looks like this: [ atoms ] ; nrtype resnr residue atom cgnr chargemasstypeB chargeB MassB 1 CT1ACECH3 1 -0.190264 12.01 CT_per -0.12033412.01 [ bonds ] ;ai aj func th0 kb th0B kbB 1 2 1 0.10900 284512.0 0.10900113804.8 [ pairs ] 1 8 1 [ angles ] ;ai ajak funct th0 kb th0B kbB 2 1 3 1 109.500 292.880 109.500117.152 . [ dihedrals ] ij kl func th0 cth mult th0B cthB multB 2 1 5 6 9180.0 2.86144 1180.01.14458 1 Now, I have created 6 different lambda values and placed a well-equilibrated structure and the same topology file (with values corresp. to lambda=0 and lambda =1) within six directories. The .mdp files contain the information (init-lambda-state=0,1,..) which lambda state is it. Is my approach correct ? Secondly, when I grompp followed by gmxdump -s *.tpr I find, that there is no difference in hamiltonian between the two. So, does the scaling take place during runtime? Third, since in state B only the hamiltonian is rescaled (the perturbed entries are defined in ffnonbonded.itp file) do I need to explicitly add another section [ pairs_nb ]? Again, I thank you for replying. On Sat, Apr 20, 2013 at 5:52 PM, Michael Shirts mrshi...@gmail.com wrote: You have to change atom types. For example: [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon h1h1 0. 0. A 2.47135e-01 6.56888e-02 h1_pert h1 0. 0. A 2.47135e-01 3.56888e-02 ; perturbed The mass and charge can be zero, because they will be defined in the [ atoms ] part [ atoms ] ; nrtype resnr residue atom cgnr chargemasstypeB chargeB MassB 1 h1 1 BLAHH1a 1 -0.0891.008h1_pert -0.030 1.008; perturbed On Sat, Apr 20, 2013 at 4:04 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Hi, I am trying to perform expanded ensemble simulations between 2 states A (lambda=0) and B (lambda =1) with 6 intermediate lambda values. In state B the Hamiltonian is rescaled, such that the epsilons of the vdW interactions, the charges, the bond, angle and dihedral constants are a multiple of the similar terms of State A. It's not quite clear to me (going through the archives of the gmx-users mailing list how to perform these calculations. One way to do this, is to use a single topology file in which the charges and the other terms are specified for both states A and B. However, it is not clear as to how should I scale the epsilons in the topology file. (My atoms are not mutated in state B. They are the same atoms with scaled epsilons.) Secondly, since I have the topology files for states A and B, is there a way I could perform the simulations (any particular way in grompp) where both the topology files can be preprocessed designating the end states and using the mdp options, the simulations corresponding to the intermediate lambda values performed?? -- 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 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 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] Free Energy Calculations in Gromacs
Hi, I am trying to perform expanded ensemble simulations between 2 states A (lambda=0) and B (lambda =1) with 6 intermediate lambda values. In state B the Hamiltonian is rescaled, such that the epsilons of the vdW interactions, the charges, the bond, angle and dihedral constants are a multiple of the similar terms of State A. It's not quite clear to me (going through the archives of the gmx-users mailing list how to perform these calculations. One way to do this, is to use a single topology file in which the charges and the other terms are specified for both states A and B. However, it is not clear as to how should I scale the epsilons in the topology file. (My atoms are not mutated in state B. They are the same atoms with scaled epsilons.) Secondly, since I have the topology files for states A and B, is there a way I could perform the simulations (any particular way in grompp) where both the topology files can be preprocessed designating the end states and using the mdp options, the simulations corresponding to the intermediate lambda values performed?? -- 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] Free Energy Calculations in Gromacs
You have to change atom types. For example: [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon h1h1 0. 0. A 2.47135e-01 6.56888e-02 h1_pert h1 0. 0. A 2.47135e-01 3.56888e-02 ; perturbed The mass and charge can be zero, because they will be defined in the [ atoms ] part [ atoms ] ; nrtype resnr residue atom cgnr chargemasstypeB chargeB MassB 1 h1 1 BLAHH1a 1 -0.0891.008h1_pert -0.030 1.008; perturbed On Sat, Apr 20, 2013 at 4:04 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Hi, I am trying to perform expanded ensemble simulations between 2 states A (lambda=0) and B (lambda =1) with 6 intermediate lambda values. In state B the Hamiltonian is rescaled, such that the epsilons of the vdW interactions, the charges, the bond, angle and dihedral constants are a multiple of the similar terms of State A. It's not quite clear to me (going through the archives of the gmx-users mailing list how to perform these calculations. One way to do this, is to use a single topology file in which the charges and the other terms are specified for both states A and B. However, it is not clear as to how should I scale the epsilons in the topology file. (My atoms are not mutated in state B. They are the same atoms with scaled epsilons.) Secondly, since I have the topology files for states A and B, is there a way I could perform the simulations (any particular way in grompp) where both the topology files can be preprocessed designating the end states and using the mdp options, the simulations corresponding to the intermediate lambda values performed?? -- 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 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] Free energy on GPU?
Dear all. I'm trying to estimate relative solvation enegry of brombenzene (relative to benzene) via thermodynamic integration. Can I perform such calculation in GROMACS with GPU acceleration? As I currently understand to make use of GPU one need to use Verlet cutoff scheme. When I do so with pme electrostatics everything works fine until free energy calculation stage. Something strange happens there: the temperature of the system increases with increase of lambda value with no respect to thermostat (300 at lambda = 0.0 - 500 at lambda = 1.0). Interesting fact that with reaction-field electrostatics everything seemed to work fine but now I cannot be sure that these results are reliable. As I understood from manual there is some issue with Verlet cutoff scheme and free energy calculations. Can I perform TI calculation in GROMACS with GPU acceleration or should I use group cutoffs and forget about GPU? Thanks a lot, Oleg Titov -- 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] Free energy on GPU?
On 4/18/13 2:30 PM, Олег Титов wrote: Dear all. I'm trying to estimate relative solvation enegry of brombenzene (relative to benzene) via thermodynamic integration. Can I perform such calculation in GROMACS with GPU acceleration? As I currently understand to make use of GPU one need to use Verlet cutoff scheme. When I do so with pme electrostatics everything works fine until free energy calculation stage. Something strange happens there: the temperature of the system increases with increase of lambda value with no respect to thermostat (300 at lambda = 0.0 - 500 at lambda = 1.0). Interesting fact that with reaction-field electrostatics everything seemed to work fine but now I cannot be sure that these results are reliable. As I understood from manual there is some issue with Verlet cutoff scheme and free energy calculations. Can I perform TI calculation in GROMACS with GPU acceleration or should I use group cutoffs and forget about GPU? As far as I am aware, free energy calculations are not supported on GPU. -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
Re: [gmx-users] Free energy landscape by g_sham
g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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] Free energy landscape by g_sham
Thank you Sir Regards kavya On Sun, Mar 31, 2013 at 11:58 AM, bipin singh bipinel...@gmail.com wrote: g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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 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] Free energy landscape by g_sham
On 2013-03-31 12:21, Kavyashree M wrote: Thank you Sir Note that the free energy differences are rigorously correct only if the array of the cells in the grid correspond units of phase space with the same volume. This is close to impossible to achieve, but the plots may still give insight. Regards kavya On Sun, Mar 31, 2013 at 11:58 AM, bipin singh bipinel...@gmail.com wrote: g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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 -- 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
[gmx-users] Free energy landscape by g_sham
Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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] free energy
Dea GROMACS Users, I want to calculate the free energy for my system, for example (Gibbs and Helmholtz), but I didn't define the free_energy in the md.mdp and my simulation has been finished!!! May I ask you that say me is there a solution fro this problem? Best Regards Sara -- 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] Free energy calculations with BAR and TI
--- On Fri, 2/11/12, Tom Kirchner tom.kirch...@strath.ac.uk wrote: Actually, this is a known problem. You should find the description and solution in the archive. I had the same problem, so this may make your search more easy :) Thank you, it's good to know I'm not doing something wrong. Indeed, changing 298.15 to 298 in the .xvg files fixed it, and the effect on the result is smaller than the statistical error, I bet. Could anyone comment on my other question (whether the BAR simulations can be used for standard TI)? Ignacio -- 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] Free energy calculations with BAR and TI
Hi Fernandez,
Actually, this is a known problem. You should find the description and
solution in the archive. I had the same problem, so this may make your
search more easy :)
The problem is in the code, at some point float and numbers are messed
up, or something in this direction.
You can either edit the code and recompile gromacs or you substitute the
temperatures with SED to a temperature nearly the same, 298 for example.
Ah, here is the link:
http://gromacs.5086.n6.nabble.com/problem-with-g-bar-td4633215.html
Best
Tom Kirchner
On 11/02/2012 10:46 AM, Ignacio Fernández Galván wrote:
Hi all,
Can I use the same simulations (with delta_lambda=0, init_lambda and
foreign_lambda) for TI and BAR calculations? I guess that boils down to whether
the simulations with foreign_lambda are in equilibrium with the init_lambda, or
they are some sort of hybrid ensemble between the different lambdas.
Whatever the answer, I have another problem. I tried a BAR calculation and got
this message with g_bar:
Fatal error:
Temperature in file 0.1.xvg different from earlier files or setting
But the temperatures are all the same:
$ grep 'T =' ?.?.xvg
0.0.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0
0.1.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0.1
0.2.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0.2
0.3.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0.3
0.4.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0.4
0.5.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0.5
0.6.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0.6
0.7.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0.7
0.8.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0.8
0.9.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 0.9
1.0.xvg:@ subtitle T = 298.15 (K), \xl\f{} = 1
Is this maybe due to some numerical rounding error?
Thanks
Ignacio
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[gmx-users] Free energy calculation on a frozen fragment
Hi all, I'm interested in calculating the free-energy change when a frozen part of the system changes. The change, in general, implies a change in coordinates and in non-bonded parameters. As far as I know, there's no efficient way to calculate this currently in gromacs. The only way I see is adding the two endpoints of the frozen fragment, and progressively turn on and off the electrostatic and vdw interactions (that is, use a dual-topology approach). This can be calculated either with TI or with BAR. But this is quite cumbersome, and it would be more efficient if one could change the frozen coordinates with lambda. Something similar can be done with position restraints, but these don't give a frozen enough geometry, and I'm not sure the results would be quite reliable. When calculating dH/dlambda with a frozen fragment, the contributions from the changing charges and non-bonded parameters are correctly included, what is missing is the contribution from the changing coordinates, and I believe this can be obtained if I can get an output of the average force (in vector form) on each affected atom. Is there some way to get this information (without storing the forces for the whole system)? Assuming that forces on frozen atoms are calculated at all. With the average force I can get the contribution to dH/dlambda, but this would only work with TI, for BAR I would need to be able to calculate the energy with different coordinates, and I'm afraid that's harder. Any other ideas on how to calculate the free energy when the coordinates of a frozen fragment change? Thanks. Ignacio -- 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] Free energy between residues
Dear Gmx Users, I want to obtain the free energy difference between the pair of residues in my protein chain with respect to thheir distance. Would combinbation: 1) g_dist - distances between two groups during the simulation time 2) g_energy -fee (DelatG - with energy groups I am interested in stated in mdp file) give me those values? Or I should use PMF - umbrella sampling with the bias (harmonic) potential introduced? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Free energy between residues
Dear Steven, Where are you working? From my experience the g_energy -fee only gives a free enrgy estimate for the whole system, so one has to pull out all the energy terms based on your index file of interest and sum them in a spread sheet. if the -fee can do the energy estimates for a specific set, please let me know this would be valuable to me. Sincerely, Stephan Watkins Original-Nachricht Datum: Thu, 28 Jun 2012 09:28:09 +0100 Von: Steven Neumann s.neuman...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: [gmx-users] Free energy between residues Dear Gmx Users, I want to obtain the free energy difference between the pair of residues in my protein chain with respect to thheir distance. Would combinbation: 1) g_dist - distances between two groups during the simulation time 2) g_energy -fee (DelatG - with energy groups I am interested in stated in mdp file) give me those values? Or I should use PMF - umbrella sampling with the bias (harmonic) potential introduced? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Free energy between residues
On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? From my experience the g_energy -fee only gives a free enrgy estimate for the whole system, so one has to pull out all the energy terms based on your index file of interest and sum them in a spread sheet. if the -fee can do the energy estimates for a specific set, please let me know this would be valuable to me. I think I will just need a potential energy between those residues (LR and Coulombic) and then can get the effective potential Ueff=-kTlne(-BU) and then g_dist. I want to extract parameters for coarse-grained simulation. Steven Sincerely, Stephan Watkins Original-Nachricht Datum: Thu, 28 Jun 2012 09:28:09 +0100 Von: Steven Neumann s.neuman...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: [gmx-users] Free energy between residues Dear Gmx Users, I want to obtain the free energy difference between the pair of residues in my protein chain with respect to thheir distance. Would combinbation: 1) g_dist - distances between two groups during the simulation time 2) g_energy -fee (DelatG - with energy groups I am interested in stated in mdp file) give me those values? Or I should use PMF - umbrella sampling with the bias (harmonic) potential introduced? Thank you, Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Free energy between residues
On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? From my experience the g_energy -fee only gives a free enrgy estimate for the whole system, so one has to pull out all the energy terms based on your index file of interest and sum them in a spread sheet. if the -fee can do the energy estimates for a specific set, please let me know this would be valuable to me. I think I will just need a potential energy between those residues (LR and Coulombic) and then can get the effective potential Ueff=-kTlne(-BU) and then g_dist. If you are using PME, there is no trivial way to decompose the reciprocal space term. -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 * Only plain text messages are allowed! * 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] Free energy between residues
On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? From my experience the g_energy -fee only gives a free enrgy estimate for the whole system, so one has to pull out all the energy terms based on your index file of interest and sum them in a spread sheet. if the -fee can do the energy estimates for a specific set, please let me know this would be valuable to me. I think I will just need a potential energy between those residues (LR and Coulombic) and then can get the effective potential Ueff=-kTlne(-BU) and then g_dist. If you are using PME, there is no trivial way to decompose the reciprocal space term. -Justin But if I will get the effective potential with respect to the distance I can adjust non bonded parameters to this curve in coarse grained model. Am I right? -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Free energy between residues
On 6/28/12 6:51 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? From my experience the g_energy -fee only gives a free enrgy estimate for the whole system, so one has to pull out all the energy terms based on your index file of interest and sum them in a spread sheet. if the -fee can do the energy estimates for a specific set, please let me know this would be valuable to me. I think I will just need a potential energy between those residues (LR and Coulombic) and then can get the effective potential Ueff=-kTlne(-BU) and then g_dist. If you are using PME, there is no trivial way to decompose the reciprocal space term. -Justin But if I will get the effective potential with respect to the distance I can adjust non bonded parameters to this curve in coarse grained model. Am I right? Honestly, I have no idea on what intend to adjust. Certainly you can tweak things in any way you like, but that doesn't mean the answer makes sense or that what you've done is justifiable. To me, umbrella sampling seems far more straightforward. -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 * Only plain text messages are allowed! * 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] Free energy between residues
I work in UK, London. Why are you asking? Because Im a super cop. No I just woundered about people with gmail, yahoo, or like mine gmx as to where they are at, etc... Ive been doing something similar, and it fits with whats expected, however what Justin said is true, without knowing what your doing, or how inclusivly your doing it, it may or may not make sense. In my case I may either be lucky, or something of the sort... That, and I was trying to post a little, as I read the post extensivly and find them helpfull sometimes...but post little other than a lame thing here and there. Stephan Watkins University of Bern, Department of Allergy, rheumatology and immunology Bern 3011 Switzerland 0041 31 632 43 22/42 33 Original-Nachricht Datum: Thu, 28 Jun 2012 07:19:14 -0400 Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Free energy between residues On 6/28/12 6:51 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? From my experience the g_energy -fee only gives a free enrgy estimate for the whole system, so one has to pull out all the energy terms based on your index file of interest and sum them in a spread sheet. if the -fee can do the energy estimates for a specific set, please let me know this would be valuable to me. I think I will just need a potential energy between those residues (LR and Coulombic) and then can get the effective potential Ueff=-kTlne(-BU) and then g_dist. If you are using PME, there is no trivial way to decompose the reciprocal space term. -Justin But if I will get the effective potential with respect to the distance I can adjust non bonded parameters to this curve in coarse grained model. Am I right? Honestly, I have no idea on what intend to adjust. Certainly you can tweak things in any way you like, but that doesn't mean the answer makes sense or that what you've done is justifiable. To me, umbrella sampling seems far more straightforward. -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 * Only plain text messages are allowed! * 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Free energy calculation about ions (hope Justin A. Lemkul can give some suggestions )
On 5/9/12 10:37 PM, DeChang Li wrote: Dear all, I want to calculate the ion solvation free energy (e.g. an ion Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR) method, following the tutorial by Justin A. Lemkul. However, if I turn off the Coulombic interaction, the total charge of my system would not neutral at all. Does this affact my calculation? I would think so. There have been numerous discussion on this topic over the years, so please consult the mailing list archive. Among the more interesting posts you're likely to find: http://lists.gromacs.org/pipermail/gmx-users/2006-September/023973.html http://lists.gromacs.org/pipermail/gmx-users/2006-March/020677.html http://lists.gromacs.org/pipermail/gmx-users/2008-February/032541.html There is published literature on ion hydration free energies, so do some literature searching to see how others handle such situations. Even a simple Google search turns up some useful information. -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/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] Free energy calculation about ions (hope Justin A. Lemkul can give some suggestions )
Dear all, I want to calculate the ion solvation free energy (e.g. an ion Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR) method, following the tutorial by Justin A. Lemkul. However, if I turn off the Coulombic interaction, the total charge of my system would not neutral at all. Does this affact my calculation? = Dechang Li , Ph.D Biomechanics and Biomaterials Laboratory Department of Applied Mechanics School of Aerospace Engineering Beijing Institute of Technology Beijing 100081, P. R. China = -- 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] Free Energy calcualtions
Hi Gromacs Users, I want to mutate a glutamate in my protein to alanine in presence of a ligand. With glutamate, the protein charge is -3. To neutralize the system, I added 3K+ ions. Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2 + 3K+). Right now I'm in the charge part of the mutation. Once this is successful, I will include the VDW mutation too. I have added the mutation details of Glu to Ala residue in the topology in [atoms], [bonds], [angles] and [dihedrals] sections. After I run the grompp command, the result says that my State_B topology has +1 charge since I am not including mutation of one K+ ion to neutral K+ ion. How can I mutate 1 particular K+ to K atom and subsequently to a dummy atom? Since I'm using OPLS force field, we have ions.itp to be used in the topology file, changing one K+ is making it troublesome for me to implement in the topology file. Any suggestions are helpful. Thanks for your time. Regards Sai -- 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] free energy calculation and g_bar error
Dear gmx-users: I was trying to do a free energy calculation of a charged ligand, according to the paper Calculation of Absolute Binding Free Energies for Charged Ligands and Effects of Long-Range Electrostatic Interactions , one of the problems with charged ligands is that the use of a solvent-solvent cutoff causes an overpolarization of the the solvent toward the solute charge, but this can be done by not using any cutoffs at all (If I did not misunderstand it). In the following, this is my part of mdp parameter for non-charged ligand: ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 ; Electrostatics coulombtype= PME rcoulomb = 1.2 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 for charged ligand, it is like this: ; Neighborsearching and short-range nonbonded interactions nstlist = 0 ns_type = simple pbc = no rlist= 0.0 ; Electrostatics coulombtype = cut-off rcoulomb = 0.0 ; van der Waals vdw-type = cut-off rvdw-switch = 0.0 rvdw = 0.0 Is this correct for what it means in the paper that by using no cutoff at all? Anyway, I presume that this is correct, and run some free energy calculation, when I used the g_bar to calculate the results, I got the error message like this : Fatal error: Some dhdl files contain only one value (dH/dl), while others contain multiple values (dH/dl and/or Delta H), will not proceed because of possible inconsistencies. So what does it mean? Thank you for answering my questions in advance. Regards Chunxia -- 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] Free energy between surfaces
Dear Gmx Users, I am wondering whether you know a technique for calculating the free energy between charged surfaces - I want to calculate distance when the deltaG=0 so that the surfaces are in equilibrium - closer distance will make that they repeal each other, longer (deltaG0). Will Umbrella Samling would be ok for those calculations? If I pull a whole surface away from another (in NPT) the box vectors will descrease to maintain the same density of water. Thus, the surface will be smaller, am I right? How about pbc? If you have any ideas, please share! Steven -- 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] Free energy between surfaces
One way to get the free energy is to measure the force as a function of distance and do the integration to get the PMF, as used in the paper: Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the Hydrophobic Interaction betweenTwo Plates. J. AM. CHEM. SOC. 2007, 129, 4678-4686 Jianguo From: Steven Neumann s.neuman...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, 18 February 2012, 17:25 Subject: [gmx-users] Free energy between surfaces Dear Gmx Users, I am wondering whether you know a technique for calculating the free energy between charged surfaces - I want to calculate distance when the deltaG=0 so that the surfaces are in equilibrium - closer distance will make that they repeal each other, longer (deltaG0). Will Umbrella Samling would be ok for those calculations? If I pull a whole surface away from another (in NPT) the box vectors will descrease to maintain the same density of water. Thus, the surface will be smaller, am I right? How about pbc? If you have any ideas, please share! Steven -- 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/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 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] Free energy between surfaces
Cheers pal! :) Steven On Sat, Feb 18, 2012 at 9:42 AM, Jianguo Li ljg...@yahoo.com.sg wrote: One way to get the free energy is to measure the force as a function of distance and do the integration to get the PMF, as used in the paper: Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the Hydrophobic Interaction between Two Plates. J. AM. CHEM. SOC. 2007, 129, 4678-4686 Jianguo -- *From:* Steven Neumann s.neuman...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, 18 February 2012, 17:25 *Subject:* [gmx-users] Free energy between surfaces Dear Gmx Users, I am wondering whether you know a technique for calculating the free energy between charged surfaces - I want to calculate distance when the deltaG=0 so that the surfaces are in equilibrium - closer distance will make that they repeal each other, longer (deltaG0). Will Umbrella Samling would be ok for those calculations? If I pull a whole surface away from another (in NPT) the box vectors will descrease to maintain the same density of water. Thus, the surface will be smaller, am I right? How about pbc? If you have any ideas, please share! Steven -- 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 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 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] Free energy tutorial 6
hi! again.. ı collect all .xvg files into a single file.. and run g_bar g_bar -f md.xvg -o -oi -oh the program gave me below result hayalet@ubuntu:~/Masaüstü$ g_bar -f md.xvg -o -oi -oh :-) G R O M A C S (-: Good ROcking Metal Altar for Chronical Sinners :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. 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. :-) g_bar (-: Option Filename Type Description -f md.xvg Input, Opt!, Mult. xvgr/xmgr file -g ener.edr Input, Opt., Mult. Energy file -obar.xvg Output, Opt! xvgr/xmgr file -oi barint.xvg Output, Opt! xvgr/xmgr file -oh histogram.xvg Output, Opt! xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -b real 0 Begin time for BAR -e real -1 End time for BAR -tempreal -1 Temperature (K) -precint2 The number of digits after the decimal point -nbmin int5 Minimum number of blocks for error estimation -nbmax int5 Maximum number of blocks for error estimation -nbinint100 Number of bins for histogram output md.xvg: 0.0 - 5000.0; lambda = 1.000 foreign lambdas: 0.000 (5250021 pts) 0.050 (5250021 pts) Writing histogram to histogram.xvg Back Off! I just backed up histogram.xvg to ./#histogram.xvg.1# No results to calculate. hayalet@ubuntu:~/Masaüstü$ Where I am doing wrong please help me .. thanks.. -- 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] Free energy tutorial 6
murat özçelik wrote: hi! again.. ı collect all .xvg files into a single file.. and run g_bar You can't do that. g_bar requires multiple input files, as I stated before. -Justin g_bar -f md.xvg -o -oi -oh the program gave me below result hayalet@ubuntu:~/Masaüstü$ g_bar -f md.xvg -o -oi -oh :-) G R O M A C S (-: Good ROcking Metal Altar for Chronical Sinners :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, nbs! p ; Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. nbs! p; 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. :-) g_bar (-: Option Filename Type Description -f nbs! p; nbsp; md.xvg Input, Opt!, Mult. xvgr/xmgr file -g ener.edr Input, Opt., Mult. Energy file -obar.xvg Output, Opt! xvgr/xmgr file -oi barint.xvg Output, Opt! xvgr/xmgr file -oh histogram.xvg Output, Opt! xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]w bool no! nbsp; View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -b real 0 Begin time for BAR -e real -1 End time for BAR -tempreal -1 Temperature (K) -precint2 The number of digits after the decimal point -nbmin int5 Minimum number of blocks for error estimation -nbmax int5 nbs! p; Maximum number of blocks for error estimation -nbinint100 Number of bins for histogram output md.xvg: 0.0 - 5000.0; lambda = 1.000 foreign lambdas: 0.000 (5250021 pts) 0.050 (5250021 pts) Writing histogram to histogram.xvg Back Off! I just backed up histogram.xvg to ./#histogram.xvg.1# No results to calculate. hayalet@ubuntu:~/Masaüstü$ Where I am doing wrong please help me .. thanks.. -- 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/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] free energy tutorial 6
hi all! ı am doing tutorial 6 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html ı have a problem.. ı am collect all md.xvg files and run g_bar with below command.. g_bar -f md.xvg -o -oi -oh.. the program gave me the following error.. Why does not consist of bar.xvg file please help me! thanks... :-) g_bar (-: Option Filename Type Description -f md.xvg Input, Opt!, Mult. xvgr/xmgr file -g ener.edr Input, Opt., Mult. Energy file -obar.xvg Output, Opt! xvgr/xmgr file -oi barint.xvg Output, Opt! xvgr/xmgr file -oh histogram.xvg Output, Opt! xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]w bool no View output .xvg, .xpm, .eps and .pdb files xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -b real 0 Begin time for BAR -e real -1 End time for BAR -tempreal -1 Temperature (K) -precint2 The number of digits after the decimal point -nbmin int5 Minimum number of blocks for error estimation -nbmax int5 Maximum number of blocks for error estimation -nbinint100 Number of bins for histogram output md.xvg: 0.0 - 5000.0; lambda = 1.000 foreign lambdas: 0.000 (5250021 pts) 0.050 (5250021 pts) Writing histogram to histogram.xvg No results to calculate. -- 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] free energy tutorial 6
murat özçelik wrote: hi all! ı am doing tutorial 6 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html ı have a problem.. ı am collect all md.xvg files and run g_bar with below command.. g_bar -f md.xvg -o -oi -oh.. the program gave me the following error.. Why does not consist of bar.xvg file You only provided a single input file (md.xvg) - g_bar requires the .xvg files of all the lambda intervals. -Justin please help me! thanks... :-) g_bar (-: Option Filename Type Description -- -- -f md.xvg Input, Opt!, Mult. xvgr/xmgr file -g ener.edr Input, Opt., Mult. Energy file -obar.xvg Output, Opt! xvgr/xmgr file -oi barint.xvg Output, Opt! xvgr/xmgr file -oh histogram.xvg Output, Opt! xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]w bool no View output .xvg, .xpm, .eps and .pdb files xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -b real 0 Begin time for BAR -e real -1 End time for BAR -tempreal -1 Temperature (K) -precint2 The number of digits after the decimal point -nbmin int5 Minimum number of blocks for error estimation -nbmax int5 Maximum number of blocks for error estimation -nbinint100 Number of bins for histogram output md.xvg: 0.0 - 5000.0; lambda = 1.000 foreign lambdas: 0.000 (5250021 pts) 0.050 (5250021 pts) Writing histogram to histogram.xvg No results to calculate. -- 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/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] Free Energy tutorial - choosing number of solvent molecules
Hello all, I'm running the same process from the free energy tutorial by Justin Lemkul... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html . How did the number of solvent particles get chosen (in the tutorial, 210 molecules were chosen)? I seem to be getting slightly different results (ranging from as small as 200 J/mol to about 5 kJ/mol depending on how many molecules I choose (ranging for example from 210 ethanol molecules to about 610 ethanol molecules for the largest energy difference change of about 5 kJ). I keep running tests to see if there is some sort of minimum atom number to get steady consistent numbers but I can't seem to find it. When I plot for example the bar.xvg barint.xvg for both sets to see where the lines don't match up, its usually one or two points that differ slightly which cause the free energies in the end to be slightly different.I seem to be noticing too that the more atoms I use, the free energy gets a little bit lower. Does anybody have any experience with this? Thanks. -- *Best regards,* ** *Fabian F. Casteblanco* *Rutgers University -- * *C: +908 917 0723* *E: **fabian.castebla...@gmail.com* fabian.castebla...@gmail.com -- 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] Free Energy tutorial - choosing number of solvent molecules
Fabian Casteblanco wrote: Hello all, I'm running the same process from the free energy tutorial by Justin Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html. How did the number of solvent particles get chosen (in the tutorial, 210 molecules were chosen)? I seem to be getting slightly different If memory serves, I reproduced what was in the original paper, but do check. results (ranging from as small as 200 J/mol to about 5 kJ/mol depending on how many molecules I choose (ranging for example from 210 ethanol molecules to about 610 ethanol molecules for the largest energy difference change of about 5 kJ). I keep running tests to see if there is some sort of minimum atom number to get steady consistent numbers but I can't seem to find it. When I plot for example the bar.xvg barint.xvg for both sets to see where the lines don't match up, its usually one or two points that differ slightly which cause the free energies in the end to be slightly different.I seem to be noticing too that the more atoms I use, the free energy gets a little bit lower. Does anybody have any experience with this? How long are your simulations? I have experienced the case (using a water-octanol solvent mixture) where the initial configuration made a big difference in the result, so longer simulations and multiple configurations for the solvent were necessary to get reliable averages. -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/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] free energy (coordinates file)
On 7/01/2012 9:12 PM, parto haghighi wrote: Dear GMX users, I have a question about 6th gromacs tutorial. That's not a useful description, because nobody else knows what list you're looking at. A URL is much better. I have to perform 5 steps of calculation contain: 1) EM-1 2) EM-2 3) NVT 4) NPT 5) Product MD for each Lambda value from 0 up to 1. I have a .gro file contains initial coordinates of my system : drg.gro For lambda = 0.00 I have done 5 steps (above) and its results is : md0.gro (from MD-Production) my question is should I use md0.gro for next calculations ( lambda = 0.05) or I have to apply drg.gro file again? Surely the tutorial mentions this. In principle, it doesn't matter because you are running a converged simulation at each lambda. In practice, it probably does matter a little because you aren't. There's probably some cancellation of errors if you start each lambda point from the same structure (and you get to run all the lambda points in parallel if you do so). 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/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] free energy (coordinates file)
Dear GMX users, I have a question about 6th gromacs tutorial. I have to perform 5 steps of calculation contain: 1) EM-1 2) EM-2 3) NVT 4) NPT 5) Product MD for each Lambda value from 0 up to 1. I have a .gro file contains initial coordinates of my system : drg.gro For lambda = 0.00 I have done 5 steps (above) and its results is : md0.gro (from MD-Production) my question is should I use md0.gro for next calculations ( lambda = 0.05) or I have to apply drg.gro file again? Thank in advance. P.Haghighi -- 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] Free Energy of a mutated molecule
Hello all,
Please if anybody can help.
I'm trying to mutate a -CH3 to an -H (I guess with 3 dummy atoms
attached to it). Below I sketched the process. I broke it up into
3 steps and I wanted to use g_bar for the actual mutation step (step
2). Does anybody have any experience with something like this? I
keep getting LINCS errors like this one:
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000378, max 0.010709 (between atoms 9 and 68)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
9 68 57.10. 0.1099 0.
9 66 90.00. 0.1122 0.
... for some of the Lambdas in the mutation part. I understand this
is a common error and it means that things are changing so my thinking
is that it is trying to rotate the dummy bonds for some reason I don't
understand. Are my steps below correct? Are dummy atoms suppose to
keep their original mass (not zero) ? Am I suppose to add parameters
for State B for these dummy atom bonds/angles also?
If anybody can help, I would greatly appreciate it. Thank you.
.--{Atom 68 (H -- Dum)}
|
R - {Atom 8 C} - {Atom 9 (C -- H)} - {Atom 66 (H -- Dum)}
|
'--{Atom 67 (H -- Dum)}
Essentially.. a R-C-[CH3] -- R-C-[H]
--
Force Field: CGenFF
STEP 1: Decoupling: -[CH3] (0 Charge, No LJ Interactions)
[ atoms ]
; nr type resnr resid atom cgnr charge
mass typeB chargeB massB
8 CG301 1 SIM C38 0.00
9 CG331 1 SIM C25 9 -0.27
12.01100 CG331 0.00 12.01100 ;
66 HGA3 1 SIM H251 66 0.09
1.00800 HGA3 0.00 1.00800 ;
67 HGA3 1 SIM H252 67 0.09
1.00800 HGA3 0.00 1.00800 ;
68 HGA3 1 SIM H253 68 0.09
1.00800 HGA3 0.00 1.00800 ;
--
STEP 2: Mutation: -[CH3] to -[H]
[ atoms ]
; nr type resnr residatomcgnrcharge
masstypeB chargeBmassB
8 CG3011SIM C38 0.00
12.01100
CG3110.0012.01100 ;
9 CG3311SIM C25 9 0.00 12.01100
HGA1 0.001.00800;
66 HGA3 1SIM H251660.00
1.00800
DUM 0.00 0.00 ;
67 HGA3 1SIM H252670.00 1.00800
DUM 0.00 0.00 ;
68 HGA3 1SIM H253680.00
1.00800DUM 0.00 0.00 ;
--
STEP 3: Coupling: -[H] (LJ Interactions, Full Charge)
[ atoms ]
; nr type resnr residatomcgnrcharge
masstypeB chargeBmassB
8 CG3111SIM C38 0.00 12.01100
CG311 -0.09 12.01100 ;
9 HGA1 1SIM C25 9 0.00
1.00800 HGA10.09 1.00800;
66 DUM 1SIM H25166 0.00 0.00
DUM0.00 0.00 ;
67 DUM 1SIM H25267 0.00 0.00
DUM 0.00 0.00 ;
68 DUM 1SIM H25368 0.00 0.00
DUM0.00 0.00 ;
--
Best regards,
Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
E: fabian.castebla...@gmail.com
--
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Re: [gmx-users] free energy and charges
parto haghighi wrote: Dear GMX users, when I want to correct charge group of one molecule I have to do calculate its free energy. I did this work by applying 6th gromacs tutorial. In this tutorial user has to assign 0 value in topology: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_138 1 ALAB CB 1 0.000 12.011 2 opls_140 1 ALABHB1 2 0.000 1.008 3 opls_140 1 ALABHB2 3 0.000 1.008 4 opls_140 1 ALABHB3 4 0.000 1.008 5 opls_140 1 ALABHB4 5 0.000 1.008 my question is when I have to zero value to its charge how can I correct my charges: Don't set your charges to zero. The tutorial states why everything is zero there - the process for which the free energy calculation is being done is a van der Waals transformation, so the charges are fixed at zero. For your calculations, you need to: 1. assign some starting value for charges (QM, chemical intuition, etc) and atom types 2. calculate DG of solvation and check the accuracy of the resulting value 3. adjust charges (and perhaps atom types) if necessary and return to step 1 -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/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] free energy and UB term
Dear GMXers, I'm trying to manually add two sets of Urey-Bradley terms to the topology file (in [angle] entry with type 5). However, it seems it is not allowed. I got the following error: Incorrect number of parameters - found 8, expected 4 or 4 for U-B. Is it true that I can't do this in gromacs? Thanks. Luke -- 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] free energy and UB term
On 16/12/2011 7:22 AM, lq z wrote: Dear GMXers, I'm trying to manually add two sets of Urey-Bradley terms to the topology file (in [angle] entry with type 5). However, it seems it is not allowed. I got the following error: Incorrect number of parameters - found 8, expected 4 or 4 for U-B. Is it true that I can't do this in gromacs? Thanks. You can add any interaction you like. What you can't get is useful help if you don't show what you've tried. :-) 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/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] free energy calculation State B has non-zero total charge: 5.800000e+01
Dear gmx users: I am using the free energy to calculate the ligand binding affinity to protein, during the decouple process, I need to put some restraint between the protein and the ligand, e.g. distance restraint. But distance restraint is only for intramolecular, so I need to make a hybrid [moleculetype] section that includes the protein and the ligand, which means the ligand sort of becoming a residue of the protein. In this case, I do not know how to put my ligand in the couple-moltype? or I need to manually put all these state B for the ligand? Anyway, so I manually put all these B-state parameters for the ligand, as I turned the B state charge to zero, when I did the grompp, it showed up a note: State B has non-zero total charge: 5.80e+01. so what does it mean? What can I do for this? Will be really appreciated for answering back. Thanks Chunxia -- 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] free energy calculation State B has non-zero total charge: 5.800000e+01
Chunxia Gao wrote: Dear gmx users: I am using the free energy to calculate the ligand binding affinity to protein, during the decouple process, I need to put some restraint between the protein and the ligand, e.g. distance restraint. But distance restraint is only for intramolecular, so I need to make a hybrid [moleculetype] section that includes the protein and the ligand, which means the ligand sort of becoming a residue of the protein. In this case, I do not know how to put my ligand in the couple-moltype? or I need to manually put all these state B for the ligand? Anyway, so I manually put all these B-state parameters for the ligand, as I turned the B state charge to zero, when I did the grompp, it showed up a note: State B has non-zero total charge: 5.80e+01. so what does it mean? What can I do for this? Will be really appreciated for answering back. I would think you could avoid all these problems by using the pull code for a restraint, rather than an intramolecular distance restraint. The error with a net charge of +58 seems to indicate that whatever you're doing to the topology is turning on (likely) every charge in the system, rather than just those of some small part of it. -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/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] Free Energy Question
Hello all, I have a general question about calculating free energies. I recently used g_bar to calculate the free energies of decoupling coulombic and vdW forces of a solute molecule in solvent. I now need to calculate the free energy of a solute molecule mutating to a new molecule (identical but with an extra -CH3 group) in a vacuum and in a solvent. Does anybody know if it would be better to use g_Bar again but this time having the extra -CH3 group completely decoupled by itself or with it be better to use the older slow-growth method that the Gromacs Manual talks about in Sec 3.12. I'm not sure if there is a way to only decouple a certain part of a molecule using the g_bar method, rather than decoupling the entire molecule. Thanks for your help. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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] Free Energy Question
I think using Perturbation method is more appropriate for this kind of free energy calculation. Check Leach, Molecular Modelling Principle and Applications pp 554-568. Its clearly described there and you can implement it in GROMACS. Cheers, Emanuel = Emanuel Birru PhD Candidate Faculty of Pharmacy and Pharmaceutical Sciences Monash University (Parkville Campus) 381 Royal Parade, Parkville Victoria 3052, Australia Tel: Int + 61 3 9903 9187 E-mail: emanuel.bi...@monash.edu www.pharm.monash.edu.au -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Fabian Casteblanco Sent: Tuesday, 4 October 2011 6:28 AM To: gmx-users@gromacs.org Subject: [gmx-users] Free Energy Question Hello all, I have a general question about calculating free energies. I recently used g_bar to calculate the free energies of decoupling coulombic and vdW forces of a solute molecule in solvent. I now need to calculate the free energy of a solute molecule mutating to a new molecule (identical but with an extra -CH3 group) in a vacuum and in a solvent. Does anybody know if it would be better to use g_Bar again but this time having the extra -CH3 group completely decoupled by itself or with it be better to use the older slow-growth method that the Gromacs Manual talks about in Sec 3.12. I'm not sure if there is a way to only decouple a certain part of a molecule using the g_bar method, rather than decoupling the entire molecule. Thanks for your help. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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 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] Free energy sampling using G_bar
Hello all, I am finished running a free energy calculation using g_bar and i followed Justin Lemkuls tutorial and I am in the process of analyzing inorder to determine if I had adequate sampling. I have read the 'BAR' paper by Bennett but there are still some concerns whether I have enough sampling (see attached). I see in the tutorial that the sampling goes up to very large sample numbers, some greater than 30,000 where mine only make it to about 300. This 'samples' refers to how many times a certain energy level was experienced? Does this mean my system should be left for longer times? My lines don't line as as closely as the Methane Decoupling tutorial do. Also, for other solvents that I used, some are giving me a warning for violating the 2nd law of thermodynamics and i noticed its because on one of the output lines, the entropy decreases a small bit, and some are giving me a free energy with a std deviation of at most 1.7 kJ/mol. Does this all mean my sampling is not enough? Thanks for your help. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com H2.agr.tar.gz Description: GNU Zip compressed 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
Re: [gmx-users] Free energy sampling using G_bar
Fabian Casteblanco wrote: Hello all, I am finished running a free energy calculation using g_bar and i followed Justin Lemkuls tutorial and I am in the process of analyzing inorder to determine if I had adequate sampling. I have read the 'BAR' paper by Bennett but there are still some concerns whether I have enough sampling (see attached). I see in the tutorial that the sampling goes up to very large sample numbers, some greater than 30,000 where mine only make it to about 300. This 'samples' refers to Sampling in the tutorial is excessive; I believe I state that in discussing the free energy output settings. how many times a certain energy level was experienced? Does this mean Yes. The output histograms show the distribution of energy values in neighboring windows. my system should be left for longer times? My lines don't line as as closely as the Methane Decoupling tutorial do. Also, for other The histograms look fine to me. Lots of overlap. solvents that I used, some are giving me a warning for violating the 2nd law of thermodynamics and i noticed its because on one of the output lines, the entropy decreases a small bit, and some are giving me a free energy with a std deviation of at most 1.7 kJ/mol. Does this all mean my sampling is not enough? Perhaps in this instance, yes, but not all of the sampling. You may have to sample a bit more in the window that's causing problems, but likely not all of them. I don't know whether uneven sampling (i.e. more points in one window relative to others) is a problem for BAR. -Justin Thanks for your help. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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/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] Free energy calculation question
Hello Justin, I'm calculating the free energy of a drug in an alcohol solvent. I have a question referring to your free energy tutorial. You mentioned that decoupling of electrostatic interactions is linear and decoupling of vdW can vary. Is this true for your case of methanol in water or for all cases? When I ran my system of drug in ethanol solvent, I got a non linear dG for both electrostatic and vdW. Also, is there no need to find dG of cav ( the free energy required to form the solute cavity within the solvent) ? I have attached some graphs. Thanks for your help. Your tutorial was extremely useful. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com dG300_summary.agr Description: application/grace dG300_summary.agr Description: application/grace -- 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] Free energy calculation question
Fabian Casteblanco wrote: Hello Justin, I'm calculating the free energy of a drug in an alcohol solvent. I have a question referring to your free energy tutorial. You mentioned that decoupling of electrostatic interactions is linear and decoupling of vdW can vary. Is this true for your case of methanol in water or for all cases? When I ran my system of drug in ethanol solvent, I got I've never seen a case where (de)coupling of Coulombic interactions wasn't linear. Since, for electrostatics, V is linearly dependent on lambda, I would expect this to generally be the case. I don't know if nonlinearity is possible; maybe someone else can comment. But generally, people use very few lambda values when (de)coupling charges from the system and linearity is generally achieved, with some minor variation towards the extreme values of lambda (close to 0 and 1). a non linear dG for both electrostatic and vdW. Also, is there no need to find dG of cav ( the free energy required to form the solute cavity within the solvent) ? I have attached some graphs. There is no explicit cavity term, but that's what happens when you turn on LJ interactions - the solute appears gradually within the solvent. -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/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] Free energy
g_lie calculates the deltaG= alpha(Vl-s LJp - Vl-s LJw) + beta(Vl-s elp - Vl-s elw) equation. But when calculating DGbind from g_lie it will ask for only one term at a time i.e. -Elj for either Vl-s LJp or Vl-s LJw and -Cqq for either Vl-s elp or Vl-s elw. My question is when using only Vl-s LJp for -Elj and Vl-s elp for -Cqq, how the LJ and EL terms calculated for ligand-water interaction or in vice-versa condition for ligand-protein interactions to complete the deltaG equation? -- 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/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] Free Energy Integrator Selection
Hi there, I am also doing FEP calculations and I am also using sd as integrator. The problem that I am having with this integrator is the temperature coupling (NTP). I am setting the targeted temperature of the system on 300K, for 2 Groups, Protein_and_ligand and Solvent. g_energy gives me 303K 301K respectably. If I use the md and noose-hover thermostat the results are 300K for both groups. For that reason I was thinking on changing to md. But afther reading the post http://lists.gromacs.org/pipermail/gmx-users/2007-February/025815.html I think that I shuold stick on sd. The questions are If by trying sd with target temperature 298K and get 300K as a result, is the simulation valid? Fabian, If you use sd the temperature of your system is the wanted one? Thanks in advance Marcelino Justin A. Lemkul jalem...@vt.edu wrote: Fabian Casteblanco wrote: Dear all, I was running free energy calculation for a drug molecule in solvent. First, For [coulomb + vdW] -- [vdW] , I used 'md' integrator For [vdW] -- [none], I was using 'md' but it required me to switch to 'sd' based on this error message: WARNING: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used. Is using sd really much more accurate? Is it best to use 'sd' for [coulomb + vdW] -- [vdW] as well? Yes. See, for instance, some of the commentary here: http://lists.gromacs.org/pipermail/gmx-users/2007-February/025815.html There are other posts regarding this topic, but I don't have the time to pull them up. -Justin Thank you. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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/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 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] Free Energy Integrator Selection
Try running for longer and look at the convergence of the temperatures over time. I suspect that what you are reporting is actually just statistical noise. I am not sure about using the sd integrator and defining multiple temperature coupling groups... If you define the same temperature for each then I suspect this is the exact same as defining the system as a single temperature coupling group (for the sd integrator). Since you can not extract dynamic information from your FE simulations anyway, the sd integrator is the best choice. Chris. -- original message -- Hi there, I am also doing FEP calculations and I am also using sd as integrator. The problem that I am having with this integrator is the temperature coupling (NTP). I am setting the targeted temperature of the system on 300K, for 2 Groups, Protein_and_ligand and Solvent. g_energy gives me 303K 301K respectably. If I use the md and noose-hover thermostat the results are 300K for both groups. For that reason I was thinking on changing to md. But afther reading the post http://lists.gromacs.org/pipermail/gmx-users/2007-February/025815.html I think that I shuold stick on sd. The questions are If by trying sd with target temperature 298K and get 300K as a result, is the simulation valid? Fabian, If you use sd the temperature of your system is the wanted one? Thanks in advance Marcelino Justin A. Lemkul jalemkul at vt.edu wrote: -- 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] Free Energy Integrator Selection
Dear all, I was running free energy calculation for a drug molecule in solvent. First, For [coulomb + vdW] -- [vdW] , I used 'md' integrator For [vdW] -- [none], I was using 'md' but it required me to switch to 'sd' based on this error message: WARNING: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used. Is using sd really much more accurate? Is it best to use 'sd' for [coulomb + vdW] -- [vdW] as well? Thank you. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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] Free Energy Integrator Selection
Fabian Casteblanco wrote: Dear all, I was running free energy calculation for a drug molecule in solvent. First, For [coulomb + vdW] -- [vdW] , I used 'md' integrator For [vdW] -- [none], I was using 'md' but it required me to switch to 'sd' based on this error message: WARNING: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used. Is using sd really much more accurate? Is it best to use 'sd' for [coulomb + vdW] -- [vdW] as well? Yes. See, for instance, some of the commentary here: http://lists.gromacs.org/pipermail/gmx-users/2007-February/025815.html There are other posts regarding this topic, but I don't have the time to pull them up. -Justin Thank you. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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/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] Free energy calculation
Hello all, I am setting up a free energy calculation (drug from full coulomb+vdW in solution -- drug with only vdW in solution -- dummy drug in solution). After reading most of the papers, I understand that you need significant overlap from the energies for each intermediate point to overlap so its best to have many intermediate points from Lambda=0 to Lambda=1. The drug molecule I have is a bit complex but I wasn't sure if using too small of an intermediate could have a bad effect on the free_energy calculation. I know Justin Lemkul said in its tutorial that Lambda=+0.05 should be good for most but I decided to go with Lambda=+0.02. Could this have any negative effect other than taking a longer time? Also, how does one come up with the best soft-core potential parameters to use? Is it ok to use the one from the Methane in water tutorial? Thanks for everyone's expertise. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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] Free energy calculation
Fabian Casteblanco wrote: Hello all, I am setting up a free energy calculation (drug from full coulomb+vdW in solution -- drug with only vdW in solution -- dummy drug in solution). After reading most of the papers, I understand that you need significant overlap from the energies for each intermediate point to overlap so its best to have many intermediate points from Lambda=0 to Lambda=1. The drug molecule I have is a bit complex but I wasn't sure if using too small of an intermediate could have a bad effect on the free_energy calculation. I know Justin Lemkul said in its tutorial that Lambda=+0.05 should be good for most but I decided to go with Lambda=+0.02. Could this have any negative effect other than taking a longer time? Also, how does one come up with the best soft-core potential parameters to use? Is it ok to use the one from the Methane in water tutorial? The settings from the methane tutorial should basically be defaults, which generally work well. Unless you have specific reason to change them, they should be fine for most purposes. I don't know if one can have too much overlap, but using BAR even 0.05 is overkill, I've found. For methods like TI you would likely need 0.05, or even less in some cases, but BAR converges better. -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/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] free energy
Dear Users ! Is it possible to calculate the free energy for a molecule , at the zero step MD , when i see the mail list this question has been posted once , but i could not find the reply for this ! is there any option for this like g_energy ! -- 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] free energy
Please see this... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html Raghu On Sun, Jul 10, 2011 at 12:33 PM, balaji nagarajan balaji_se...@hotmail.com wrote: Dear Users ! Is it possible to calculate the free energy for a molecule , at the zero step MD , when i see the mail list this question has been posted once , but i could not find the reply for this ! is there any option for this like g_energy ! -- 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 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] free energy calculations
Hi, I want to run free energy calculations on a particular protein-ligand complex. I do not have much knowledge on this so I have some questions, hopefully someone might give me clear answers. I am following the tutorial given in this link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html My questions are as follows: 1. I am assuming that I do not need the protein without the ligand form for free energy calculations. Am I right? 2. To use g_bar, I need to run the protein-ligand complex with a) first with lambda ranging from 0.5 to 1 for vdw coupling and b) followed by lambda ranging from 0.5 to 1 for coulombic coupling Adding these would give the deltaG I am looking for. Am I right? 3. Are there any papers that use g_bar function in gromacs to calculate free energy? Thanks in advance, Raghu -- 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] free energy calculations
Ragothaman Yennamalli wrote: Hi, I want to run free energy calculations on a particular protein-ligand complex. I do not have much knowledge on this so I have some questions, hopefully someone might give me clear answers. I am following the tutorial given in this link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html My questions are as follows: 1. I am assuming that I do not need the protein without the ligand form for free energy calculations. Am I right? Free energy calculations can be done on a number of systems. The tutorial is just one simple example. 2. To use g_bar, I need to run the protein-ligand complex with a) first with lambda ranging from 0.5 to 1 for vdw coupling and b) followed by lambda ranging from 0.5 to 1 for coulombic coupling Adding these would give the deltaG I am looking for. Am I right? No. The range for lambda should be 0 to 1. Using 0.5 to 1 gives only part of the free energy for the transformation, and not necessarily half. 3. Are there any papers that use g_bar function in gromacs to calculate free energy? The g_bar tool is relatively new to Gromacs, so maybe not. The BAR method itself has been around for decades though, so its applications have been demonstrated in the literature many times. -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/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] free energy
Hi all I have performed a PMF simulation of taking part of a molecule out of the cavity of a host using umbrella sampling. The free energy curve suggests that the guest prefers to be outside the host as the bound state is higher in energy, or the free energy difference to go in is positive. However when I view the trajectories for each window it appears that there is always more bound states than unbound. This leads me to doubt my free energy profile? Cheers Gavin -- 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] free energy
Your windows are restrained. The PMF that you get out of WHAM is a representation of the relative sampling after removing the umbrella biases. Sounds like you are saying that you look at the still-biased trajectories and you see different a different distribution of states than you do in the de-biased PMF. not sure what the problem is here. Perhaps go back to some review literature on US. Now, if you saw more bound than unbound in unrestrained simulations, then that's a different story, but that doesn't appear to be what you are talking about. Chris. -- original message -- Hi all I have performed a PMF simulation of taking part of a molecule out of the cavity of a host using umbrella sampling. The free energy curve suggests that the guest prefers to be outside the host as the bound state is higher in energy, or the free energy difference to go in is positive. However when I view the trajectories for each window it appears that there is always more bound states than unbound. This leads me to doubt my free energy profile? Cheers Gavin -- 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] free energy
Hi Chris My windows are restrained obviously using the force constant in the mdp file. The trajectories that I have viewed are those of the individual biased sampling windows. I have not put on the unbiased simulations yet. There is also the following issue: The simulations involve two identical molecules containing hydrocarbon chains. I calculate the PMF to take a specific hydrocarbon chain of one molecule out of a specific site on the neighbouring molecule. When this guest chain goes out, other chains can go in (intramolecular or intermolecular). Will this affect the profile? Gavin chris.ne...@utoronto.ca wrote: Your windows are restrained. The PMF that you get out of WHAM is a representation of the relative sampling after removing the umbrella biases. Sounds like you are saying that you look at the still-biased trajectories and you see different a different distribution of states than you do in the de-biased PMF. not sure what the problem is here. Perhaps go back to some review literature on US. Now, if you saw more bound than unbound in unrestrained simulations, then that's a different story, but that doesn't appear to be what you are talking about. Chris. -- original message -- Hi all I have performed a PMF simulation of taking part of a molecule out of the cavity of a host using umbrella sampling. The free energy curve suggests that the guest prefers to be outside the host as the bound state is higher in energy, or the free energy difference to go in is positive. However when I view the trajectories for each window it appears that there is always more bound states than unbound. This leads me to doubt my free energy profile? Cheers Gavin -- 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] free energy
yes it will, and so will it affect the profile if water molecules or ions go in when both chains are absent. You'll need to determine what question you are trying to answer and also think pretty hard about what your PMF really means in the context of this system. Chris. -- original message -- Hi Chris My windows are restrained obviously using the force constant in the mdp file. The trajectories that I have viewed are those of the individual biased sampling windows. I have not put on the unbiased simulations yet. There is also the following issue: The simulations involve two identical molecules containing hydrocarbon chains. I calculate the PMF to take a specific hydrocarbon chain of one molecule out of a specific site on the neighbouring molecule. When this guest chain goes out, other chains can go in (intramolecular or intermolecular). Will this affect the profile? Gavin -- 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] free energy
The current simulations are currently in vacuum. Does the following mdp file seem ok. Note that this is a production run using the final configuration after a lengthy equilibration. Also I was thinking about trying to prevent the other chains from entering the specific site; is there a a way to implement this in gromacs. Gavin chris.ne...@utoronto.ca wrote: yes it will, and so will it affect the profile if water molecules or ions go in when both chains are absent. You'll need to determine what question you are trying to answer and also think pretty hard about what your PMF really means in the context of this system. Chris. -- original message -- Hi Chris My windows are restrained obviously using the force constant in the mdp file. The trajectories that I have viewed are those of the individual biased sampling windows. I have not put on the unbiased simulations yet. There is also the following issue: The simulations involve two identical molecules containing hydrocarbon chains. I calculate the PMF to take a specific hydrocarbon chain of one molecule out of a specific site on the neighbouring molecule. When this guest chain goes out, other chains can go in (intramolecular or intermolecular). Will this affect the profile? Gavin umbrella81.mdp Description: application/mdp -- 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] free energy
Dear Gavin: I'm not seeing a lot of effort on your part to answer these questions. I suspect that you can answer some of this. Good luck! Chris. -- original message -- The current simulations are currently in vacuum. Does the following mdp file seem ok. Note that this is a production run using the final configuration after a lengthy equilibration. Also I was thinking about trying to prevent the other chains from entering the specific site; is there a a way to implement this in gromacs. Gavin chris.neale at utoronto.ca wrote: yes it will, and so will it affect the profile if water molecules or ions go in when both chains are absent. You'll need to determine what question you are trying to answer and also think pretty hard about what your PMF really means in the context of this system. Chris. -- original message -- Hi Chris My windows are restrained obviously using the force constant in the mdp file. The trajectories that I have viewed are those of the individual biased sampling windows. I have not put on the unbiased simulations yet. There is also the following issue: The simulations involve two identical molecules containing hydrocarbon chains. I calculate the PMF to take a specific hydrocarbon chain of one molecule out of a specific site on the neighbouring molecule. When this guest chain goes out, other chains can go in (intramolecular or intermolecular). Will this affect the profile? Gavin -- 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] free energy perturbation
Hello, I am doing free energy perturbation for ethane to methanol conversion. Can anybody tell me which of the following way is right to define virtual site for hydrogen? [ virtual_sites2 ] 3 2 1 1 0.00 or [ virtual_sites2 ] 3 2 1 1 1.00 Thanking you in anticipation. With regards, Jignesh -- 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] Free energy calculation and position restraint
Dear all From Table 5.6 of Gromacs 4.5.4 manu, position restrain constants can be interpolated in free energy calculations. However, I cannot find how to set up this. Can somebody help? thanks. dawei -- 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] free energy-couple-intramol options
Hello, I read through the couple-intramol options (yes and no) good many times but I can not still realize what is the difference and which option I should select. I am having a hydrocarbon system (polyethylene in hexane as solvent). Can anyone help me understand these options please? (in plain english) option yes, says something about FF of large molecules which is my case...but I dont see the statement: nb interactions might lead to kinetically trapped vaccum conformations?! Also, as with the electrostatics treatment in my hydrocarbon system I am still unsure if I need to include electrostatics potentials. I digged into the literature and found the following articles containing nonpolar polymers where vdw is the only nonbonded term in the FF. http://pubs.acs.org/doi/abs/10.1021/ma9600419 http://www.sciencedirect.com/science?_ob=ArticleURL_udi=B6TXW-40TY56F-16_user=458507_coverDate=11%2F30%2F2000_rdoc=1_fmt=high_orig=search_origin=search_sort=d_docanchor=view=c_searchStrId=1650178009_rerunOrigin=google_acct=C22002_version=1_urlVersion=0_userid=458507md5=bf0b74cfc76e0dafbadf06396fb63745searchtype=a Please let me know your comments Thanks Moeed -- 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] free energy blank dgdl
Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file: There are 0 atoms and 0 charges for free energy perturbation EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr output.grompp_em mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v output.mdrun_em MD grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n PE-HEX.ndx output.grompp_md mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x md-l0.xtc -dgdl md-l0.dgdl -v output.mdrun_md with mdp : pbc = xyz energygrps = PE HEX ;Run control integrator = md dt = 0.002 nsteps = 50 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.1 rcoulomb= 1.1 ;1.0 rvdw= 1.0 ;Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ;0.1 ref_t = 400 ;300 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs ; Free energy control stuff free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no *** Thank you in advance. Moeed -- 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] free energy blank dgdl
Moeed wrote: Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file: There are 0 atoms and 0 charges for free energy perturbation EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr output.grompp_em mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v output.mdrun_em MD grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n PE-HEX.ndx output.grompp_md mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x md-l0.xtc -dgdl md-l0.dgdl -v output.mdrun_md with mdp : pbc = xyz energygrps = PE HEX ;Run control integrator = md dt = 0.002 nsteps = 50 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME By not setting a proper coulombtype, grompp defaults to cutoff, which is a very inaccurate method. vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.1 rcoulomb= 1.1 ;1.0 rvdw= 1.0 ;Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ;0.1 ref_t = 400 ;300 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs ; Free energy control stuff free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no You didn't set couple-moltype so mdrun doesn't know which molecule to decouple. -Justin *** Thank you in advance. Moeed -- 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/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] free energy blank dgdl
hi It seems that your couple-moltype is missing, that is, no molecules will be turned off interaction. dawei On Thu, Feb 17, 2011 at 8:26 AM, Moeed lecie...@googlemail.com wrote: Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file: There are 0 atoms and 0 charges for free energy perturbation EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr output.grompp_em mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v output.mdrun_em MD grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n PE-HEX.ndx output.grompp_md mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x md-l0.xtc -dgdl md-l0.dgdl -v output.mdrun_md with mdp : pbc = xyz energygrps = PE HEX ;Run control integrator = md dt = 0.002 nsteps = 50 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.1 rcoulomb= 1.1 ;1.0 rvdw= 1.0 ;Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ;0.1 ref_t = 400 ;300 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs ; Free energy control stuff free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no *** Thank you in advance. Moeed -- 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 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] free energy
One other thing I would point out is that the solvation free energy is dependent on concentration. you will get a different result with 4 polymer chains vs 3 vs 3, etc. Make sure you understand the dependence. Also, the free energy will depend on the polymer chain length. Polymer and finite concentration calculations are harder to interpret than monomer and infinite dilution calculations. Make sure you understand the differences. I'm not sure understand all of them, though, so you'll have to think about it yourself! Basically, you need to make sure the physical picture of the molecules in gromacs is the physical picture of the realistic molecular system itself. On Mon, Feb 14, 2011 at 6:28 PM, Moeed lecie...@googlemail.com wrote: Dear experts, I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consisting of 4 polymer chains and 480 hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3). 1- For such a study I dont know how many polymers I need to have in my system. If FE can be done with only one chain, am I making system bigger in vain? Does this matter affect the accuracy of results? 2- I have switched off electrostatics so I am using free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no In David Mobley's turorial the last three lines are not included. I wanted to know if I am to run say 10 simulations for different lambda, what purpose does the last three lines serve in 4.0.7 ? I got very close values in that tutorial without these settings. ( I know what these lines mean, just curious how these three lines affect the results in 4 X +). Please let me know your comments/point of view about the system and setting I am using. Thanks Moeed -- 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/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 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] free energy
Dear experts, I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consisting of 4 polymer chains and 480 hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3). 1- For such a study I dont know how many polymers I need to have in my system. If FE can be done with only one chain, am I making system bigger in vain? Does this matter affect the accuracy of results? 2- I have switched off electrostatics so I am using free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no In David Mobley's turorial the last three lines are not included. I wanted to know if I am to run say 10 simulations for different lambda, what purpose does the last three lines serve in 4.0.7 ? I got very close values in that tutorial without these settings. ( I know what these lines mean, just curious how these three lines affect the results in 4 X +). Please let me know your comments/point of view about the system and setting I am using. Thanks Moeed -- 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] free energy
How close are the polymers in space? On February 14, 2011 at 3:28 PM Moeed lecie...@googlemail.com wrote: Dear experts, I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consisting of 4 polymer chains and 480 hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3). 1- For such a study I dont know how many polymers I need to have in my system. If FE can be done with only one chain, am I making system bigger in vain? Does this matter affect the accuracy of results? 2- I have switched off electrostatics so I am using free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no In David Mobleys turorial the last three lines are not included. I wanted to know if I am to run say 10 simulations for different lambda, what purpose does the last three lines serve in 4.0.7 ? I got very close values in that tutorial without these settings. ( I know what these lines mean, just curious how these three lines affect the results in 4 X +). Please let me know your comments/point of view about the system and setting I am using. Thanks Moeed TJ Mustard Email: musta...@onid.orst.edu -- 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] free energy
On February 14, 2011 at 3:28 PM Moeed lecie...@googlemail.com wrote: Dear experts, I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consisting of 4 polymer chains and 480 hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3). 1- For such a study I dont know how many polymers I need to have in my system. If FE can be done with only one chain, am I making system bigger in vain? Does this matter affect the accuracy of results? How close are the polymers? 2- I have switched off electrostatics so I am using free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no In David Mobleys turorial the last three lines are not included. I wanted to know if I am to run say 10 simulations for different lambda, what purpose does the last three lines serve in 4.0.7 ? I got very close values in that tutorial without these settings. ( I know what these lines mean, just curious how these three lines affect the results in 4 X +). Have you thought of using Bennetts Acceptance Ratio? This make for a little more work but knowledge of your error is nice. Please let me know your comments/point of view about the system and setting I am using. Thanks Moeed TJ Mustard Email: musta...@onid.orst.edu -- 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] free energy calculation , grompp crash
Dear users I tried free energy calculation but grompp couldn't go through. It stops after *** Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning H bonds into constraints... Coupling 1 copies of molecule type 'Protein' *** The CPU usage is 100%. I just add following into the mdp file: *** free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 couple-moltype = Protein couple-lambda0 = vdw-q couple-lambda1 = none *** Does anyone have some idea about this problem? thanks. Another question is whether I can switch off two molecules (such as protein+ligand) in free energy calculation? I searched this list and got that 4.0.7 did support this. how about 4.5.4? dawei -- 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] Free energy
The biotin-streptavidin interaction is on the order of -75 kJ/mol, so a binding free energy of -300 kJ/mol (dissociation constant of 10^-52 M) means something is fundamentally wrong - start by taking a hard look at your protocol, as convergence problems wouldn't account for that kind of deviation. From: mohsen ramezanpour ramezanpour.moh...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, 29 December, 2010 20:36:59 Subject: [gmx-users] Free energy Dear All I estimated protein-ligand free energy about -300 kj Is it logical?I think it is wrong.what do you think? what is the range of correct value for a typical protein-ligand? protein=660 residue ligand=25 atom water=4670 Na=118 Cl=120 thanks in advance -- 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] Free energy
Dear All I estimated protein-ligand free energy about -300 kj Is it logical?I think it is wrong.what do you think? what is the range of correct value for a typical protein-ligand? protein=660 residue ligand=25 atom water=4670 Na=118 Cl=120 thanks in advance -- 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] Free energy
mohsen ramezanpour wrote: Dear All I estimated protein-ligand free energy about -300 kj Is it logical?I think it is wrong.what do you think? There is no way for anyone on this list to assess such things. It sounds unphysical to me, but that's just a gut reaction based on nothing in particular. what is the range of correct value for a typical protein-ligand? Look into the literature. Surely you're not the first to attempt such a calculation. -Justin protein=660 residue ligand=25 atom water=4670 Na=118 Cl=120 thanks in advance -- 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/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] Free energy
In addition to Justin's comments, check your convergence with block averaging. Is there a systematic energy drift as you increase the amount of sampling prior to each block? Also, try applying your method to Na+ and Cl- in a box of water. If you can't get that free energy correctly, then you certainly cannot get the free energy you are looking at given the method and amount of sampling. Finally, check on your ions. You've got a lot of them, so chances are that they exist near the binding site in some of your simulations. Have you converged the ion distribution? This can be harder than you expect. Chris. -- original message -- Dear All I estimated protein-ligand free energy about -300 kj Is it logical?I think it is wrong.what do you think? what is the range of correct value for a typical protein-ligand? protein=660 residue ligand=25 atom water=4670 Na=118 Cl=120 thanks in advance -- next 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] free energy of methan disappearing:tutorial
Yeah there is so much to do. 1. Build a methane in a program that allows saving of pdb. Make sure the pdb and all the atoms are correctly formated. Or find a methane pdb or gro file. I think there is one off of Dr. Mobelys website. 2. yes (you dont even need a state_B) 3. no (gromacs 4.5.x will take care of it if you setup your mdp file correctly) 4. All you need to do is read the free energy perturbation section in the manual. You will change the settings of your mdp file (under fep) and your off. I got some rather nice values. I know read the manual is the go to phrase here, but it works 95% of the time for me. On December 21, 2010 at 2:08 AM mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I want to calculate protein-drug binding free energy. I read Dr.Mobley tutorial(about free energy of methan dissapearing from water).I couldnt understand some of its parts. Can I use thisr tutorial in this case(protein-drug)? Besides, I have a few question about that: 1-What do I need to use as my .top .gro files in my commands?(with regarding my problem)docked state or separated state?for example he has used methan(separated from water). 2-Are these files(.top .gro) the same for all values of lambda? 3-Do these files(.top .gro)change if you inversed the meaning of lambda=1 lambda=0? 4-How did he define for (with which parameters) Gromacs that lambda=1 is relating to completely interacting lambda=0 is relating to methan disappearing system? Please let me know the answer of my questions Thank in advance for your reply Sincerely yours Mohsen TJ Mustard Email: musta...@onid.orst.edu -- 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] free energy of methan disappearing:tutorial
Dear Mustard Thanks very much for your useful notes and your reply Mohsen On Tue, Dec 28, 2010 at 7:48 PM, TJ Mustard musta...@onid.orst.edu wrote: Yeah there is so much to do. 1. Build a methane in a program that allows saving of pdb. Make sure the pdb and all the atoms are correctly formated. Or find a methane pdb or gro file. I think there is one off of Dr. Mobely's website. 2. yes (you don't even need a state_B) 3. no (gromacs 4.5.x will take care of it if you setup your mdp file correctly) 4. All you need to do is read the free energy perturbation section in the manual. You will change the settings of your mdp file (under fep) and your off. I got some rather nice values. I know read the manual is the go to phrase here, but it works 95% of the time for me. On December 21, 2010 at 2:08 AM mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I want to calculate protein-drug binding free energy. I read Dr.Mobley tutorial(about free energy of methan dissapearing from water).I couldn't understand some of it's parts. Can I use thisr tutorial in this case(protein-drug)? Besides, I have a few question about that: 1-What do I need to use as my .top .gro files in my commands?(with regarding my problem)docked state or separated state?for example he has used methan(separated from water). 2-Are these files(.top .gro) the same for all values of lambda? 3-Do these files(.top .gro)change if you inversed the meaning of lambda=1 lambda=0? 4-How did he define for (with which parameters) Gromacs that lambda=1 is relating to completely interacting lambda=0 is relating to methan disappearing system? Please let me know the answer of my questions Thank in advance for your reply Sincerely yours Mohsen TJ Mustard Email: musta...@onid.orst.edu -- 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 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
