[gmx-users] Bug (?) with FEP while using particle decomposition in charge transformation
Dear all, I have faced a very strange results while using the FEP together with particle decomposition in charge transformation. Situation is as follows: gromacs-4.5.5, single precision, mpi-run on 32 nodes; only charges are modified in the topology file (VdW and massess remains the same for A and B state); particle decomposition (-pd) option is used. The combination of this conditions lead to a very strange *.xvg file like this (lambda=0): @TYPE xy @ subtitle "T = 300 (K), \xl\f{} = 0" @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "dH/d\xl\f{} \xl\f{} 0" @ s1 legend "\xD\f{}H \xl\f{} 0.1" 0. 7.74067 -2.30013 0.0200 8.83184 -2.08346 0.0400 6.61338 -2.43848 0.0600 3.85357 -2.58843 0.0800 9.49265 -2.03448 0.1000 2.4197 -2.7838 0.1200 4.81406 -2.64074 0.1400 3.79622 -2.83082 0.1600 4.9235 -2.53202 0.1800 7.24284 -2.41357 0.2000 3.79017 -2.68861 0.2200 7.84849 -2.26953 0.2400 10.1044 -2.11132 0.2600 1.89623 -3.10296 0.2800 11.6953 -2.08701 0.3000 11.103 -1.96233 0.3200 4.68676 -2.62905 0.3400 9.83457 -2.11386 0.3600 6.12451 -2.27113 0.3800 8.56351 -2.17592 0.4000 11.0368 -1.93516 0.4200 4.80366 -2.49621 0.4400 9.58472 -2.08431 0.4600 5.04113 -2.60035 The usual file (obtained without -pd) looks like this: @ title "dH/d\xl\f{}, \xD\f{}H" @ xaxis label "Time (ps)" @ yaxis label "(kJ/mol)" @TYPE xy @ subtitle "T = 300 (K), \xl\f{} = 0" @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "dH/d\xl\f{} \xl\f{} 0" @ s1 legend "\xD\f{}H \xl\f{} 0.1" 0. 7.77708 0.777688 0.0200 10.322 1.03217 0.0400 8.82036 0.882043 0.0600 9.46574 0.946536 0.0800 10.2726 1.02731 0.1000 12.0395 1.20386 0.1200 6.85707 0.685689 0.1400 8.99015 0.899035 0.1600 8.68244 0.868208 0.1800 8.98454 0.898397 0.2000 9.21256 0.921202 0.2200 7.16041 0.716125 0.2400 5.1431 0.514307 0.2600 3.34832 0.334797 0.2800 3.14324 0.314328 0.3000 1.83755 0.183755 0.3200 3.91737 0.391783 0.3400 5.79081 0.579126 0.3600 4.92766 0.492766 0.3800 8.06557 0.806605 0.4000 7.00964 0.700994 0.4200 12.1488 1.21481 So the signs of the dH/dlambda are opposite while using particle decomposition. There is no such problem while running VdW transformation. Is it a Gromacs bug or I'm doing something wrong? With best regards, Alexey Zeifman -- 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] Domain decomposition in FEP
Dear all, I'm trying to run FEP calculation of the ligand in the protein in water. Performing NVT-dynamics for Lennard-Johnes perturbation using soft core results in the following error: There is no domain decomposition for 20 nodes... I've checked out the log-file and found this: >Initial maximum inter charge-group distances: > two-body bonded interactions: 1.474 nm, Bond, atoms 4371 4391 > multi-body bonded interactions: 0.522 nm, Ryckaert-Bell., atoms 3747 3756 >Minimum cell size due to bonded interactions: 1.621 nm >Guess for relative PME load: 0.29 >Will use 20 particle-particle and 12 PME only nodes >This is a guess, check the performance at the end of the log file >Using 12 separate PME nodes >Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 >Optimizing the DD grid for 20 cells with a minimum initial size of 2.026 nm >The maximum allowed number of cells is: X 3 Y 3 Z 3 > ->-- >Program mdrun_mpi, VERSION 4.5.1 >Source code file: domdec.c, line: 6428 >Fatal error: >There is no domain decomposition for 20 nodes that is compatible with the >given box and a minimum cell size of 2.02621 nm >Change the number of nodes or mdrun option -rdd or -dds >Look in the log file for details on the domain decomposition >For more information and tips for troubleshooting, please check the GROMACS >website at http://www.gromacs.org/Documentation/Errors ->--> I understand that distance of 1.474 nm is rather big for bond! BUT I can't find such a distance between atoms 4371 4391. The fragment of gro-file for such index interval looks like this: 640LIG C4 4371 2.897 3.416 3.072 640LIG N3 4372 3.296 3.109 3.434 640LIG N6 4373 3.416 2.999 3.595 640LIG C6 4374 2.696 2.762 3.601 640LIG C7 4375 3.025 3.232 3.150 640LIG C8 4376 3.208 3.142 3.338 640LIG C9 4377 2.758 2.644 3.649 640LIG C10 4378 2.767 2.884 3.595 640LIG N4 4379 3.319 2.826 3.731 640LIG C11 4380 2.968 2.768 3.677 640LIG C12 4381 2.894 2.648 3.686 640LIG C13 4382 2.901 2.887 3.638 640LIG N5 4383 3.100 2.766 3.707 640LIG C14 4384 3.420 2.908 3.693 640LIG O1 4385 3.018 3.627 3.068 640LIG C15 4386 3.028 3.095 3.182 640LIG C16 4387 3.123 3.049 3.275 640LIG O2 4388 2.566 2.759 3.559 640LIG O3 4389 2.699 2.993 3.545 640LIG O4 4390 2.680 2.530 3.655 640LIG C17 4391 2.791 3.426 3.184 640LIG C18 4392 2.834 3.453 2.937 and the actual distance is 1.55 A - quite OK for single C-C bond. And another interesting fact is that it doesn't occur during FEP calculation of the same system without soft-core and aimed at only charge perturbation. I will appreciate any help regarding this. Alexey Zeifman -- 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] Fw: Normal mode analysis
How can I obtain normal frequencies and normal modes? How are normal frequencies and normal modes connected with eigenvalues and eigenvectors? Calculation of the system of 3000 atoms with g_nmeig gives 3000 eigenvectors which consists of 3000 coords instead of 9000*9000, why? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fw: Amber to OPLS
Is there any tool to create OPLS topology or obtain charges or is there any library of such topologies (compound of interest: BCL (bacteriochlorophyll) and lycopene? Can I use charges from Amber in OPLS? Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Double precision gives infinite force while single doesn't
Hi! When I'm using double precision calculations, for instance minimization with mdrun_d, I receive infinite forces on the 1 atom each time. But running simple mdrun with quite the same parameters results in normal minimization. I've compiled source code of gromacs-3.3.3, gromacs-4.0 and i always have this problem. Maybe there's some hints for compiling double precision version in Mandriva 2008? Thank you, Alexey Zeifman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php