[gmx-users] g_wham error analysis hangs
Hi, I have a problem with the error analysis of g_wham. The PMF profile and sampling windows looks good, but when I try to generate error bars g_wham hangs. This is what I do: g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist -nBootstrap 50 -bins 50 -bs-method traj-gauss -bsres -ac yes -bsprof -vbs This is the output after which it just hangs: Estimating integrated autocorreltion times ... [100%] ... done Back Off! I just backed up iact.xvg to ./#iact.xvg.4# Wrote iact.xvg win 0, aver = 3.413503 sig = 0.091051 win 1, aver = 3.440995 sig = 0.060213 win 2, aver = 3.536864 sig = 0.069048 win 3, aver = 3.462364 sig = 0.041276 win 4, aver = 3.508488 sig = 0.041967 win 5, aver = 3.474703 sig = 0.038848 win 6, aver = 3.546181 sig = 0.042018 win 7, aver = 3.558158 sig = 0.047886 win 8, aver = 3.870348 sig = 0.053350 win 9, aver = 3.895024 sig = 0.047226 win 10, aver = 3.905363 sig = 0.039718 win 11, aver = 3.989860 sig = 0.048854 win 12, aver = 4.033406 sig = 0.045494 win 13, aver = 4.077549 sig = 0.042215 win 14, aver = 4.096139 sig = 0.036315 win 15, aver = 4.174044 sig = 0.040574 win 16, aver = 4.119622 sig = 0.052487 win 17, aver = 4.177672 sig = 0.036798 win 18, aver = 4.148724 sig = 0.033967 win 19, aver = 4.228320 sig = 0.039398 win 20, aver = 4.161365 sig = 0.039424 win 21, aver = 4.176532 sig = 0.041844 win 22, aver = 4.224519 sig = 0.030001 win 23, aver = 4.468429 sig = 0.046136 win 24, aver = 4.536401 sig = 0.049635 win 25, aver = 4.666026 sig = 0.054179 win 26, aver = 4.670022 sig = 0.045487 win 27, aver = 4.866098 sig = 0.046887 win 28, aver = 4.935376 sig = 0.050013 win 29, aver = 4.891905 sig = 0.042927 Getting initial potential by integration. Initialized rapid wham stuff (contrib tolerance 3.3e-08) Evaluating only 474 of 1500 expressions. 1) Maximum change 2.849816e-01 100) Maximum change 2.216439e-03 200) Maximum change 1.866839e-03 300) Maximum change 1.612522e-03 400) Maximum change 1.419577e-03 500) Maximum change 1.266497e-03 600) Maximum change 1.140793e-03 700) Maximum change 1.034780e-03 800) Maximum change 9.434951e-04 900) Maximum change 8.635977e-04 1000) Maximum change 7.927633e-04 1100) Maximum change 7.293254e-04 1200) Maximum change 6.720574e-04 1300) Maximum change 6.200347e-04 1400) Maximum change 5.725450e-04 1500) Maximum change 5.290277e-04 1600) Maximum change 4.890329e-04 1700) Maximum change 4.521924e-04 1800) Maximum change 4.181996e-04 1900) Maximum change 3.867947e-04 2000) Maximum change 3.577540e-04 2100) Maximum change 3.308822e-04 2200) Maximum change 3.060068e-04 2300) Maximum change 2.829734e-04 2400) Maximum change 2.616429e-04 2500) Maximum change 2.418887e-04 2600) Maximum change 2.235951e-04 2700) Maximum change 2.066558e-04 2800) Maximum change 1.909727e-04 2900) Maximum change 1.764550e-04 3000) Maximum change 1.630186e-04 3100) Maximum change 1.505854e-04 3200) Maximum change 1.390827e-04 3300) Maximum change 1.284431e-04 3400) Maximum change 1.186038e-04 3500) Maximum change 1.095063e-04 3600) Maximum change 1.010962e-04 3700) Maximum change 9.332302e-05 3800) Maximum change 8.613974e-05 3900) Maximum change 7.950267e-05 4000) Maximum change 7.337121e-05 4100) Maximum change 6.770765e-05 4200) Maximum change 6.247700e-05 4300) Maximum change 5.764678e-05 4400) Maximum change 5.318686e-05 4500) Maximum change 4.906931e-05 4600) Maximum change 4.526823e-05 4700) Maximum change 4.175964e-05 4800) Maximum change 3.852131e-05 4900) Maximum change 3.553267e-05 5000) Maximum change 3.277469e-05 5100) Maximum change 3.022973e-05 5200) Maximum change 2.788151e-05 5300) Maximum change 2.571494e-05 5400) Maximum change 2.371608e-05 5500) Maximum change 2.187205e-05 5600) Maximum change 2.017093e-05 5700) Maximum change 1.860172e-05 5800) Maximum change 1.715425e-05 5900) Maximum change 1.581912e-05 6000) Maximum change 1.458767e-05 6100) Maximum change 1.345187e-05 6200) Maximum change 1.240432e-05 6300) Maximum change 1.143820e-05 6400) Maximum change 1.054720e-05 6500) Maximum change 9.725497e-06 6600) Maximum change 8.967716e-06 6700) Maximum change 8.268901e-06 6800) Maximum change 7.624473e-06 6900) Maximum change 7.030212e-06 7000) Maximum change 6.482219e-06 7100) Maximum change 5.976900e-06 7200) Maximum change 5.510938e-06 7300) Maximum change 5.081272e-06 7400) Maximum change 4.685081e-06 7500) Maxi
[gmx-users] REMD run on higher nodes.
Greetings I'm running REMD of 96 replicas where the run.pbs is the following: #!/bin/tcsh #PBS -S /bin/tcsh #PBS -l walltime=00:15:00 #PBS -q workq #PBS -l select=8:ncpus=12:mpiprocs=12 #PBS -l place=scatter:excl #PBS -V # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR setenv MPI_GROUP_MAX 1024 setenv MPI_UNBUFFERED_STDIO 1 #mpiexec_mpt -np 24 ./exefile mpiexec_mpt -np 96 /lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend So each replica runs at one processor. Now, I want to run the remd at 16 nodes ( double ) so that each replica is subjected to 2 processors. Kindly assist ! 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
[gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1
Hi, I effectively refer to the MSD of the protein. My simulation is different compared to the simulation of a lipid bilayer and the "normal" MSD for a protein in water should be equivalent to the red plot. I forgot to mention but the MSD are obtained from 10 ns NVE simulations. Regards, Guillaume -- View this message in context: http://gromacs.5086.x6.nabble.com/Mean-Square-Displacement-gromacs-4-5-Vs-gromacs-4-6-1-tp5010317p5010331.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] Re: energy conservation / frozen atoms
> On 8/2/13 3:19 PM, S. Alireza Bagherzadeh wrote: > > Thanks for your notes. > > > > > > I did a diagnosis test which could be of relevance here. > > > > I set up the following system: > > [ gas | liquid water (solid water) liquid water | gas ] > > > > gas is united atom methane. > > liquid water is tip4p-ice model and solid water is a cage-like > crystalline > > structure of water and methane called gas hydrate. > > > > Now, in order to test the effect of freezing and position restraining on > > the performance of nve I did two tests at 370 K. > > > > Test 1 (freezing): > > Solid water was kept frozen in all 3 dimensions (Y Y Y). > > First I ran a nvt for 250 ps for equilibration (potential and total > energy > > both converged after 250 ps, Pressure equilibrated at ~ 3950 bar). Then I > > started a 1ns nve. > > Similar to my other simulation, the total energy linearly decreased > (0.84% > > per ns) as well as potential energy. Pressure remained around 3950 bar; > > however, the temperature decreased from 370 to 364 K (physically, this > > should not happen). > > > > > > Test 2 (position restraining): > > Oxygen of solid water was strongly restrained to a point (fc of 10). > > Similar to the previous test, first I ran a nvt for 250 ps for > > equilibration (potential and total energy both converged after 250 ps, > > Pressure equilibrated at about 0 bar with fluctuations of ~ 2000 bar). > Then > > I started a 1ns nve. > > Again, similar to test 1, the total energy linearly decreased (1.33% per > > ns) as well as potential energy. Pressure remain around 0 bar; however, > the > > temperature initially dropped from 370 K to 355K within 1 ps, then > > increased to 358 K during the next 50 ps and thereafter kept linearly > > decreasing to 353 K until the end of 1 ns run (physically and > intuitively, > > this should not happen). > > > > > > > > (In both of the tests, I kept the methane inside the cages of solid > water > > position-restrained to a point by fc = 1000). > > > > If needed I can post the .mdp and .top files too. > > > > An .mdp file would be useful, otherwise a demonstration that these > parameters > actually produce an energy-conserving NVE ensemble for a simple system. > > -Justin > > -- > Here is the .mdp file for freeze test: ;-; ;-; ; Run control integrator = md ; Leap-frog algorithm tinit= 0; starting time [ps] dt = 0.001; time step [ps] nsteps = 100 ; number of steps nstcomm = 100 ; frequency for center of mass motion removal [steps] ;-; ;-; ; Output control nstxout = 0; frequency to write coordinates to output trajectory file [steps] nstvout = 0; frequency to write velocities to output trajectory file [steps] nstfout = 0; frequency to write forces to output trajectory file [steps] nstlog = 500 ; frequency to write energies to log file [steps] nstenergy= 500 ; frequency to write energies to energy file [steps] nstxtcout= 0; frequency to write coordinates to xtc trajectory [steps] xtc-precision= 1000 ; precision to write to xtc trajectory [real] xtc_grps = HYDW HYDG SOL GAS energygrps = HYDW HYDG SOL GAS ;-; ;-; ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ; frequency to update the neighbor list [steps] ns_type = grid ; (grid / simple) search for neighboring list pbc = xyz ; priodic boundary conditions (xyz / no / xy) rlist= 1.7 ; cut-off distance for the short-range neighbor list [nm] ;-; ;-; ; Electrostatics coulombtype = PME-Switch rcoulomb_switch = 1.3 ; where to switch the Coulomb potential [nm] rcoulomb = 1.5 ; distance for the Coulomb cut-off [nm] ;-; ;
Re: [gmx-users] Invalid order for directive atomtypes
Hi Jonathan, The itp's for the ligands were given atomtype sections, but atomtypes (and other *types) may only be defined before any moleculetype definition (check chapter 5 of the manual for the topology format). You'll need to remove anything before the moleculetype directive from the itp files and make sure that all the atomtypes (and other *types) referred to are correct according to the listing in the force field. Hope it helps, Tsjerk On Sun, Aug 4, 2013 at 8:46 AM, Jonathan Saboury wrote: > PDB file used :http://www.rcsb.org/pdb/explore.do?structureId=1cx2 > Commands used: http://pastebin.com/raw.php?i=YYG5ad7A > Compressed folder containing all files (10.2 MB): > http://www.sendspace.com/file/rka8ei > > So I want to simulate this complex. I am having problems with the .itp's > and do not know why. > > I get the error: > > Program grompp, VERSION 4.5.5 > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/topio.c, line: 656 > > Fatal error: > Syntax error - File NAG_GMX.itp, line 3 > Last line read: > '[ atomtypes ]' > > > Here is the logic I used while trying to get teh simulation to work, please > let me know if this is correct, because there wasn't a tutorial example > like this. > > 1.) Separate the complexed pdb into teh standard residues and ligands, so > "ATOM", "HEM", "NAG" and "S58"in this case. > > 2.) There are multiple ligands in the pdb, so I need to delete all but one > molecule and create a forcefield .itp so I can include it in the .top file. > > 3.) Once the .itp's for the single molecules are created, you need to put > the complex back together. I was having problems with adding charges, so I > only added hydrogen’s to the ligands and created complex.pdb from the new > pdb files created from acpype. > > 4.) Minimize, relax waters, then simulate. > > So what did I do wrong here? 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 > -- Tsjerk A. Wassenaar, Ph.D. -- 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
