From owner-chemistry@ccl.net Fri Feb 4 12:12:00 2011 From: "Vincent Leroux vincent.leroux\a/loria.fr" To: CCL Subject: CCL: problem in running configuration file using NAMD Message-Id: <-43866-110204120439-7603-ndv3qeih0h67/N+8t+b8AA**server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 04 Feb 2011 18:04:30 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux---loria.fr] Hi, Look at the bottom of the parameter file. What you have been doing is: - 100 minimization steps - assign velocities for 302 K all of a sudden - 2500 steps of MD 100 steps of minimization is probably not enough, but this is not the problem. You just go straight from minimization to MD: MD is started with a random set of velocities averaged to T = 302 K, resulting in your system being literally torn apart. The RATTLE algorithm tries to compensate for abnormal bond lengths occurring at the very first MD step, but of course it fails. You should do some equilibration after minimization... The comment at the beginning of your parameter file is mistaking: it says "minimization and equilibration" and below I see the (right) comment "do langevin dynamics". Seems like this input file was messed up by careless copy-paste operations. Regards VL Le 04/02/11 06:59, neha khan diya.khan.05(~)gmail.com a écrit : > Sent to CCL by: "neha khan" [diya.khan.05~~gmail.com] > Respected Sir, > When i run minimization, the program stopped abnormally. What is wrong with my file? > > REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN. > TCL: Running for 2500 steps > ERROR: Constraint failure in RATTLE algorithm for atom 2775! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2729! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1739! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2926! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6029! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2398! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2202! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3201! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 5028! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2390! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 553! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3136! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4966! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1588! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4118! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1275! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 771! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1069! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4008! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 867! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 919! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3447! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6355! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4747! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 332! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6837! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 82! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1542! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1254! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9773! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1193! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3739! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9465! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 953! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10527! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3678! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 117! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8745! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9881! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10838! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 7839! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8262! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9955! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10206! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8881! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10080! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8404! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8589! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8450! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8308! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8580! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8572! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Exiting prematurely; see error messages above. > ==================================================== > > WallClock: 74.289345 CPUTime: 74.199997 Memory: 99.713013 MB > Program finished. > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > Killed > > Below is my configuration file: > > > ############################################################# > ## JOB DESCRIPTION ## > ############################################################# > > # Minimization and Equilibration of > # pgl in a Water Sphere > > > ############################################################# > ## ADJUSTABLE PARAMETERS ## > ############################################################# > > structure ../common/pgl_ws.psf > coordinates ../common/pgl_ws.pdb > > set temperature 302 > set outputname pgl_ws_eq > > firsttimestep 0 > > > ############################################################# > ## SIMULATION PARAMETERS ## > ############################################################# > > # Input > paraTypeCharmm on > parameters ../common/par_all27_prot_lipid.inp > temperature $temperature > > > # Force-Field Parameters > exclude scaled1-4 > 1-4scaling 1.0 > cutoff 12. > switching on > switchdist 10. > pairlistdist 13.5 > > > # Integrator Parameters > timestep 2.0 ;# 2fs/step > rigidBonds all ;# needed for 2fs steps > nonbondedFreq 1 > fullElectFrequency 2 > stepspercycle 10 > > > # Constant Temperature Control > langevin on ;# do langevin dynamics > langevinDamping 5 ;# damping coefficient (gamma) of 5/ps > langevinTemp $temperature > langevinHydrogen off ;# don't couple langevin bath to hydrogens > > > # Output > outputName $outputname > > restartfreq 500 ;# 500steps = every 1ps > dcdfreq 250 > outputEnergies 100 > outputPressure 100 > > > ############################################################# > ## EXTRA PARAMETERS ## > ############################################################# > > # Spherical boundary conditions > sphericalBC on > sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423 > sphericalBCr1 26.0 > sphericalBCk1 10 > sphericalBCexp1 2 > > > ############################################################# > ## EXECUTION SCRIPT ## > ############################################################# > > # Minimization > minimize 100 > reinitvels $temperature > > run 2500 ;# 5ps> > >