Re: [gmx-users] Gromos54a8
Dear Rajat Desikan, I recently ported the 54A8 to Gromacs format. However I did not have the time yet to extensively test it or compare it to published results. I did the porting by hand (the differences between 54A7 and 54A8 are modest), which is of course more error prone. I'll send you the files off list. If you would want to check and test them, that would be of great value for me too. And after that the force field could of course be shared with the greater Gromacs community. Groetnis, Djurre H. de Jong, PhD Theory of complex systems group Westfällische Wilhelms-Universität Münster On Thursday, 24 October 2013, 15:18, rajat desikan rajatdesi...@gmail.com wrote: Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgz**http**://www.gromacs.org/@api/** deki/**files/74/= http://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzht**tp://www.gromacs.org/@api/** deki/files/74/=**ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -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 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing list gmx-users@gromacs.org
Re: [gmx-users] Gromos54a8
Thank you so much, Djurre. I will do some tests with protein-membrane systems in mind and share it with the community. I will see if I can reproduce the results in the 54A8 paper. On Fri, Oct 25, 2013 at 1:01 PM, Djurre de Jong-Bruinink djurredej...@yahoo.com wrote: Dear Rajat Desikan, I recently ported the 54A8 to Gromacs format. However I did not have the time yet to extensively test it or compare it to published results. I did the porting by hand (the differences between 54A7 and 54A8 are modest), which is of course more error prone. I'll send you the files off list. If you would want to check and test them, that would be of great value for me too. And after that the force field could of course be shared with the greater Gromacs community. Groetnis, Djurre H. de Jong, PhD Theory of complex systems group Westfällische Wilhelms-Universität Münster On Thursday, 24 October 2013, 15:18, rajat desikan rajatdesi...@gmail.com wrote: Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgz**http**://www.gromacs.org/@api/** deki/**files/74/= http://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzht**tp://www.gromacs.org/@api/** deki/files/74/=**ConvertGromos2Gromacs.tgz http://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -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 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A.
[gmx-users] Optimizing performance mac osx
Hi, I am relatively new to the gromacs environment and would like to optimize performance for my mac pro (osx 10.6.8) with 8 cores (16 in hyper-theading). I´ve read that one can use the g_tune_pme, i guess with np = 16. Don´t know if using mpirun or gromacs compiled mpi would be faster. I guess sin gromacs 4,5 mpirun is deprecated and mdrun automatically distributes the workload through all the cores, i think. We also have a 40 core condor cluster; would setting it up there increase performance? I think also that the scaling depends on the number of atoms. Any info on this? Thank very much Tiago -- 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] Wall potential for a membrane-simulation
Hi everyone! I'm new to Gromacs and trying to simulate a membrane system with two walls, one at the bottom of my box at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS version 4.5.5). My testing system consists of a membrane in the middle, water and sodium ions (40) above the membrane and water and chloride ions (also 40) beneath it. First, I built up the system, did an energy minimization and then implemented the walls for the nvt-equilibration. I didn't change anything in the topology. (Do I have to define the wall-atem-type there? If yes, what exactly do I have to put in the topology?) My nvt.mdp file looks like that: title = NVT equilibration for KALP15-DPPC define = -DSTRONG_POSRES -DPOSRES_LIPID ; position restrain the lipid ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = lipid SOL_NA_CL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions ;wall nwall = 2 wall_type = 10-4 wall_density = 100 100 wall_atomtype = C C wall_r_linpot = 1 1 ; with -1 I got a fatal error, because atoms were beyond the wall wall_ewald_zfac = 3 ewald_geometry= 3dc pbc = xy ; Periodic Boundary Conditions in x/y direction ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 303 ; temperature for Maxwell distribution gen_seed= -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions
[gmx-users] 2D umbrella sampling simulation
unfortunately not. It will be done eventually though: to follow the progress of that feature, check out: http://redmine.gromacs.org/issues/1346 If you have to do that, there is a patch that I posted on that same redmine page (posts 8 and 9) to allow this in gromacs 4.0.5. Chris. -- original message -- Thanks for your check. Yes, it should be pull_group2 for C. In this case, the two distances have a reference group B. What about the case in which no common reference group is shared with the two distances, e.g. distance1 is defined as A-B and distance2 as C-D? Can current gromacs codes perform 2D umbrella sampling for this problem? Many thanks. Mingjun -- 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] Optimizing performance mac osx
On Fri, Oct 25, 2013 at 11:19 AM, Tiago Gomes tiagogome...@gmail.comwrote: Hi, I am relatively new to the gromacs environment and would like to optimize performance for my mac pro (osx 10.6.8) with 8 cores (16 in hyper-theading). I´ve read that one can use the g_tune_pme, i guess with np = 16. Don´t know if using mpirun or gromacs compiled mpi would be faster. Won't be. GROMACS's default built-in thread-MPI is designed for this case. Do check out http://www.gromacs.org/Documentation/Acceleration_and_parallelization I guess sin gromacs 4,5 mpirun is deprecated and mdrun automatically distributes the workload through all the cores, i think. We also have a 40 core condor cluster; would setting it up there increase performance? Using more than one node for the same simulation is not useful unless you have a high-speed network, e.g. Infiniband. A network over which one would use Condor would generally not be suitable. I think also that the scaling depends on the number of atoms. Any info on this? Depends very much on the hardware, compiler, model physics and simulation composition, also. You should aim for something at least around 500-800 atoms per physical core, though. 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] GPU-gromacs
Dear prof., i want install gromacs on a multi-core workstation with a GPU(tesla c2075), should i install the openmpi or mpich2? -- 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] GPU-gromacs
On Oct 25, 2013, at 4:07 PM, aixintiankong aixintiank...@126.com wrote: Dear prof., i want install gromacs on a multi-core workstation with a GPU(tesla c2075), should i install the openmpi or mpich2? If you want to run Gromacs on just one workstation with a single GPU, you do not need to install an MPI library at all! Carsten -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] energy drift - comparison of double and single precision
Dear Xavier, 2013/10/12 XAvier Periole x.peri...@rug.nl Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? FYI, I tried 10 and 1 and the energy drift is exactly the same. Similar flags apply to temperature and pressure and I believe might seriously affect energy conservation. XAvier. On Oct 12, 2013, at 0:50, Mark Abraham mark.j.abra...@gmail.com wrote: Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are some comparative numbers at http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather different but they share the use of SETTLE. Note that using md-vv guarantees the 2007 paper is inapplicable, because GROMACS did not have a velocity Verlet integrator back then. Sharing the .log files might be informative. Mark On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi, sorry for my last post! I re-write my e-mail (with some additional information) and I provide the links to my files ;-) I compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3 lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3 ... and what I found was quite ... disturbing (see the plots of the total energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! Here is the link to the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so you can check what mdp options I used. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 2013/10/11 Mark Abraham mark.j.abra...@gmail.com On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! I join the ‘mdout.mdp’ file so you can check what mdp options I used. Maybe. Unfortunately we cannot configure the mailing list to allow people to send attachments to thousands of people, so you will need to do something like provide links to files on a sharing service. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Yes, as you have no doubt read in the papers published by the GROMACS team. Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 ... which is six years old, examining the properties of code seven years old. Life has moved on! :-) Even if you have found a problem, it is a big assumption that this is (still) the cause. 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 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 list
[gmx-users] Lie method for binding free energy calculations
Hello dears searching through literature, many cases of LIE method application for BFE calculation of small molecules are on hand . but I couldn't find any report of using this method for interaction of small peptides and proteins. I wanted to know if the protocol prepared in Justin tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html) can be used in such case? and if so, should I apply any constrain on rotatable bonds of peptide along the simulation within the non-bonded state? best, Sajad -- 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] Lie method for binding free energy calculations
On 10/25/13 11:07 AM, Sajad Ahrari wrote: Hello dears searching through literature, many cases of LIE method application for BFE calculation of small molecules are on hand . but I couldn't find any report of using this method for interaction of small peptides and proteins. I wanted to know if the protocol prepared in Justin tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html) can be used in such case? and if so, should I apply any constrain on rotatable bonds of peptide along the simulation within the non-bonded state? PMF or MM/PBSA calculations are far better suited for studying these types of interactions. -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] Lie method for binding free energy calculations
On 10/25/13 11:32 AM, Sajad Ahrari wrote: thanks for replying. are these features available under Gromacs? and is there any tutorial or related material I can grasp to stand up for start? My umbrella sampling tutorial covers generating a PMF. MM/PBSA is just a post-processing technique, requiring software external to Gromacs. The MD itself is no different and can be done with Gromacs. -Justin On Friday, October 25, 2013 6:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/25/13 11:07 AM, Sajad Ahrari wrote: Hello dears searching through literature, many cases of LIE method application for BFE calculation of small molecules are on hand . but I couldn't find any report of using this method for interaction of small peptides and proteins. I wanted to know if the protocol prepared in Justin tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html) can be used in such case? and if so, should I apply any constrain on rotatable bonds of peptide along the simulation within the non-bonded state? PMF or MM/PBSA calculations are far better suited for studying these types of interactions. -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 mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- == 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] Lie method for binding free energy calculations
On 10/25/13 11:43 AM, Sajad Ahrari wrote: is AMBER facilities the only way of approaching MM-PBSA calculations? could you lead me to any other software more friendly with Gromacs MD output? See what Google tells you. -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] Lie method for binding free energy calculations
Hi, You can email me we have a tool for mmpbsa with gromacs Andrea Messaggio inviato dal mio ASUS MeMO Pad Justin Lemkul jalem...@vt.edu ha scritto: On 10/25/13 11:43 AM, Sajad Ahrari wrote: is AMBER facilities the only way of approaching MM-PBSA calculations? could you lead me to any other software more friendly with Gromacs MD output? See what Google tells you. -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
Re: [gmx-users] energy drift - comparison of double and single precision
Hi, all- At this point, any fixes are going to be in the 5.0 version, where the integrators will be a bit different. If you upload your system files to redmine.gromacs.org (not just the .mdp), then I will make sure this gets tested there. On Fri, Oct 25, 2013 at 10:14 AM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Dear Xavier, 2013/10/12 XAvier Periole x.peri...@rug.nl Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? FYI, I tried 10 and 1 and the energy drift is exactly the same. Similar flags apply to temperature and pressure and I believe might seriously affect energy conservation. XAvier. On Oct 12, 2013, at 0:50, Mark Abraham mark.j.abra...@gmail.com wrote: Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are some comparative numbers at http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather different but they share the use of SETTLE. Note that using md-vv guarantees the 2007 paper is inapplicable, because GROMACS did not have a velocity Verlet integrator back then. Sharing the .log files might be informative. Mark On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi, sorry for my last post! I re-write my e-mail (with some additional information) and I provide the links to my files ;-) I compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3 lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3 ... and what I found was quite ... disturbing (see the plots of the total energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! Here is the link to the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so you can check what mdp options I used. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 2013/10/11 Mark Abraham mark.j.abra...@gmail.com On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! I join the ‘mdout.mdp’ file so you can check what mdp options I used. Maybe. Unfortunately we cannot configure the mailing list to allow people to send attachments to thousands of people, so you will need to do something like provide links to files on a sharing service. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Yes, as you have no doubt read in the papers published by the GROMACS team. Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 ... which is six years old, examining the properties of code seven years old. Life has moved on! :-) Even if you have found a problem, it is a big assumption that this is (still) the cause. 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 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
