[gmx-users] removal of the initial periodicity by editconf
Dear Justin I study your tutorial ( KALP15 in DPPC). You had said Convert the dppc128.pdb to .gro format with editconf and remove the initial periodicity. Which of following lines shows removal of the initial periodicity: 1) editconf -f dppc128.pdb -o dppc128.gro 2) editconf -f dppc128.pdb -o dppc128.gro -pbc 3) editconf -f dppc128.pdb -o dppc128.gro -nopbc Any help will highly appreciated. -- 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] removal of the initial periodicity by editconf
Dear Justin Excuse me for my previous question. I should use trjconv to remove initial periodicity. But I have another problem: when I use editconf -f dppc128.pdb -o dppc128.gro I encounter with Fatal error: Unknown atomtype OW I did all steps based on tutorial. What is the problem? Best Regards -- 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] removal of the initial periodicity by editconf
Excuse me. when I use grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I encounter with Fatal error: Unknown atomtype OW -- 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] removal of the initial periodicity by editconf
On 6/22/13 8:59 AM, Andrew Bostick wrote: Excuse me. when I use grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I encounter with Fatal error: Unknown atomtype OW Apparently something has gone wrong when editing the force field files. I don't know what would have led you to remove OW, though. Please go back and follow the procedure very carefully. -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] Gromacs GPU system question
Hello, I am assembling a GPU workstation to run MD simulations, and I was wondering if anyone has any recommendation regarding the GPU/CPU combination. From what I can see, the GTX690 could be the best bang for my buck in terms of number of cores, memory, clock rate. But being a dual GPU card, I was wondering if there is any latency issue that could make its performances less favorable with respect to a GTX Titan. Also, which motherboard, CPU is recommendable for this system. Thank you in advance for you help, Al -- 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] Gromacs GPU system question
On 22.06.2013 17:31, Mare Libero wrote: I am assembling a GPU workstation to run MD simulations, and I was wondering if anyone has any recommendation regarding the GPU/CPU combination. From what I can see, the GTX690 could be the best bang for my buck in terms of number of cores, memory, clock rate. But being a dual GPU card, I was wondering if there is any latency issue that could make its performances less favorable with respect to a GTX Titan. Also, which motherboard, CPU is recommendable for this system. The most important aspect to consider (by far) is, in my humble opinion, *your specific workload*: - Size of the simulation box / number of atoms, - Specific force field/required integrator (verlet?), - Handling of long range electrostatics (pme/RF/coulomb). Furthermore, the effect of the CPU is, imho, much more pronounced. Remember, mdrun-gpu doesn't 'run' on the GPU (as, e.g., HOOMD does) but loads work-sets up to the GPU, runs them, and loads them back. For example: in one box, I have an AMD FX-8350 and a GTX-660Ti available for tests, and I didn't see the GPU load going much over 60%, even with millons of atoms. Here, small differences in the potential/force field used by the model will probably change the performance of the GPU-related parts significantly (due to cu-offs and buffering schemes). Regards M. -- 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] Gromacs GPU system question
On 22.06.2013 22:18, Mare Libero wrote: The vendor I contacted was pushing for one of the high end i7 processors with hyper-threading. But from what I can read, most of the MD software don't make any use of it. So, using a the multi-cores AMD (like your FX-8350) can be a cheaper and more advantageous option. Your vendor is, in my opinion, right. The AMD consumer multicores (Piledriver) aren't actually eight-core cpus, but rather similar to 4 core cpus (they are called 'modules'). For testing a user-defined potential, I once compiled performance figures over a range of actual commodity hardware (available to me). These are all workstations and usually overclocked somehow by the students (but only if there's no crash at all in a year ;-) This is all *without GPU*, only the plain and raw CPU processing power for Gromacs is checked for (last column). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Test case: Two coarse-grained implicit-solvent vesicles bumping into each other SD integrator 480,000 particles Box (110nm)³ User-defined potential (rc=0.8225nm) dt=0.020ps CPU ArchCores ns/day - X6/1090T;3.3GHz SSE26C/6T 19.130 - FX-8350;4.5GHz AVX_FMA 4M/8T 34.175 - i7/2600K;4.2GHz AVX_256 4C/8T 39.073 - i7/3770K;4.4GHz AVX_265 4C/8T 41.931 - i7/3930K;4.2GHz AVX_256 6c/12T 56.891 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - You can see here, for CPU performance, you can't really choose anything different from the 6-core i7/3930K. It costs some bucks more than the 4-core-CPUs but will run significantly faster the time you use it. Most of what we do is protein-protein interactions and protein stability studies with explicit water/ions. One of our projects now has 100,000 atoms in a 100 Ang water box (7,800 protein atoms + 67,000 water). It's difficult to be more specific on the parameters since each project is different, but in general we do not deviate much from a standard NPT run. 10nm box/75K atoms is not very large. I guess you'd use a time step of 0.002 ps and a united atom model + spc or spc/e water? 100ns/day seem possible with any GPU from GTX-660 or higher. If you buy a mighty GPU (Titan), the question will be: can your n-core-CPU saturate such a fast GPU monster? A good compromise would be, probably, the GTX-780 which is a slightly reduced Titan for half the price and all options open. my € 0.02 M. -- 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] Re: free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2
Hi Justin, Thank you for sharing your experience with me. As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box and I am able to reproduce a similar result ( DG= -9.30 kJmol-1). Gromacs ver 4.5.5 and 4.6.2 both are compiled from source codes, while Gromacs ver 4.5.7 as reported earlier is installed with pre-compiled binary files. Thus, Gromacs ver 4.5.7 is now re-compiled again by myself. Below are shown results. In addition, L-BFGS mdp file works well for all versions after it is modified by adding define = -DFLEXIBLE. Gromacs ver 4.5.5 (compiled from source codes) point 0.050 - 0.100, DG -0.04 +/- 0.00 point 0.100 - 0.150, DG -0.08 +/- 0.00 point 0.150 - 0.200, DG -0.13 +/- 0.01 point 0.200 - 0.250, DG -0.19 +/- 0.00 point 0.250 - 0.300, DG -0.27 +/- 0.00 point 0.300 - 0.350, DG -0.35 +/- 0.00 point 0.350 - 0.400, DG -0.43 +/- 0.01 point 0.400 - 0.450, DG -0.55 +/- 0.01 point 0.450 - 0.500, DG -0.71 +/- 0.01 point 0.500 - 0.550, DG -0.94 +/- 0.00 point 0.550 - 0.600, DG -1.25 +/- 0.00 point 0.600 - 0.650, DG -1.40 +/- 0.01 point 0.650 - 0.700, DG -1.29 +/- 0.01 point 0.700 - 0.750, DG -1.01 +/- 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 0.050 - 1.000, DG -9.30 +/- 0.03 Gromacs ver 4.5.7 (compiled from source codes) lambda 0.000 - 0.050, DG 0.05 +/- 0.00 lambda 0.050 - 0.100, DG 0.02 +/- 0.00 lambda 0.100 - 0.150, DG -0.04 +/- 0.00 lambda 0.150 - 0.200, DG -0.09 +/- 0.00 lambda 0.200 - 0.250, DG -0.14 +/- 0.01 lambda 0.250 - 0.300, DG -0.21 +/- 0.01 lambda 0.300 - 0.350, DG -0.29 +/- 0.01 lambda 0.350 - 0.400, DG -0.37 +/- 0.00 lambda 0.400 - 0.450, DG -0.48 +/- 0.01 lambda 0.450 - 0.500, DG -0.65 +/- 0.01 lambda 0.500 - 0.550, DG -0.89 +/- 0.01 lambda 0.550 - 0.600, DG -1.19 +/- 0.01 lambda 0.600 - 0.650, DG -1.34 +/- 0.01 lambda 0.650 - 0.700, DG -1.23 +/- 0.00 lambda 0.700 - 0.750, DG -0.95 +/- 0.01 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 0.19 +/- 0.00 lambda 0.950 - 1.000, DG 0.38 +/- 0.00 total 0.000 - 1.000, DG -8.19 +/- 0.03 After comparing the output from ver 4.5.5 with that from ver 4.5.7, I do find quirky information from the g_bar in ver 4.5.7. In ver 4.5.7, for example, it shows that ver 4.5.7 dose not give information of dH/dl (see below) Moreover, I also try g_bar of ver 4.5.5 or 4.6.2 to process the output data (such as md*.xvg generated by ver 4.5.7). The result is unchanged and DG ( -8.19 kJmol-1) remains incorrect. Thanks, Dwey ++ g_bar ver 4.5.7, md0.05.xvg: 0.0 - 5000.0; lambda = 0.050 foreign lambdas: 0.050 (250001 pts) 0.000 (250001 pts) 0.100 (250001 pts) md0.15.xvg: 0.0 - 5000.0; lambda = 0.150 foreign lambdas: 0.150 (250001 pts) 0.100 (250001 pts) 0.200 (250001 pts) md0.1.xvg: 0.0 - 5000.0; lambda = 0.100 foreign lambdas: 0.100 (250001 pts) 0.050 (250001 pts) 0.150 (250001 pts) . . . g_bar ver 4.5.5 or 4.6.2, md0.05.xvg: 0.0 - 5000.0; lambda = 0.05 dH/dl foreign lambdas: dH/dl (250001 pts) delta H to 0 (250001 pts) delta H to 0.1 (250001 pts) md0.15.xvg: 0.0 - 5000.0; lambda = 0.15 dH/dl foreign lambdas: dH/dl (250001 pts) delta H to 0.1 (250001 pts) delta H to 0.2 (250001 pts) md0.1.xvg: 0.0 - 5000.0; lambda = 0.1 dH/dl foreign lambdas: dH/dl (250001 pts) delta H to 0.05 (250001 pts) delta H to 0.15 (250001 pts) . . . 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,
