Re: error running min

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Feb 03 2015 - 08:32:57 CST

Dear Ms Uciechowska,

These kinds of errors usually mean that there is something wrong with
how you built your system or in the minimization. It may be that you
didn't run minimization long enough (I usually do a couple thousand
rather than just 100). Otherwise, it could be a problem with the size
of the system or some kind of clash that the minimizer didn't work
out. It can help to look at which atoms are involved in error in VMD
(selection "serial 146 270 532")

Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Tue, Feb 3, 2015 at 8:23 AM, Urszula Uciechowska
<urszula.uciechowska_at_biotech.ug.edu.pl> wrote:
>
> Dear namd users,
>
> I want to run MD simulations of the DNA-protein complex. During the
> minimization I am getting an error message:
>
>
>
> RESSURE: 99 10731.6 191.359 769.037 191.359 11866.8 -117.473 769.037
> -117.473 11668.2
> GPRESSURE: 99 13089.3 233.036 1070.8 170.059 13957.7 -328.039 1217.48
> -37.0102 13888
> ENERGY: 99 37247.5702 16922.0187 4534.2241
> 211.6177 -404403.0066 89202.3123 0.0000 0.0000
> 0.0000 -256285.2636 0.0000 -256285.2636
> -256285.2636 0.0000 11422.2056 13644.9963
> 1157625.0000 11422.2056 13644.9963
>
> LDB: ============= START OF LOAD BALANCING ============== 50.2813
> LDB: Largest compute 34 load 0.297668 is 6.8% of average load 4.379461
> LDB: Average compute 0.036585 is 0.8% of average load 4.379461
> LDB: TIME 50.2822 LOAD: AVG 4.37946 MAX 5.40094 PROXIES: TOTAL 427 MAXPE
> 20 MAXPATCH 6 None MEM: 176.457 MB
> LDB: TIME 50.2841 LOAD: AVG 4.37946 MAX 4.58958 PROXIES: TOTAL 427 MAXPE
> 20 MAXPATCH 6 TorusLB MEM: 176.457 MB
> LDB: ============== END OF LOAD BALANCING =============== 50.3
> Info: useSync: 1 useProxySync: 0
> LDB: =============== DONE WITH MIGRATION ================ 50.3354
> PRESSURE: 100 10731.6 191.359 769.037 191.359 11866.8 -117.473 769.037
> -117.473 11668.2
> GPRESSURE: 100 13089.3 233.037 1070.8 170.059 13957.7 -328.039 1217.48
> -37.0102 13888
> Info: Initial time: 24 CPUs 0.134836 s/step 0.780302 days/ns 176.457 MB
> memory
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 100 37247.5702 16922.0187 4534.2241
> 211.6177 -404403.0063 89202.3123 0.0000 0.0000
> 0.0000 -256285.2633 0.0000 -256285.2633
> -256285.2633 0.0000 11422.2056 13644.9963
> 1157625.0000 11422.2056 13644.9963
>
> REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
> TCL: Running for 8000 steps
> ERROR: Constraint failure in RATTLE algorithm for atom 1460!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 270!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 532!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely; see error messages above.
> ====================================================
>
> the input file was:
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Minimization and Equilibration of
> # Ubiquitin in a Water Box
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ssb.psf
> coordinates ssb.pdb
>
> set temperature 310
> set outputname ssb_wb_eq
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters par_all36_na.prm
> parameters par_all36_prot.prm
> parameters par_water_ions_na.prm
>
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 14
> switching on
> switchdist 10.0
> pairlistdist 16.0
>
>
> # 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 1 ;# damping coefficient (gamma) of 1/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 105.0 0. 0.0
> cellBasisVector2 0.0 105.0 0.0
> cellBasisVector3 0.0 0 105.0
> cellOrigin 51.7 51.8 49.6
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSpacing 1.0
>
> #manual grid definition
> #PMEGridSizeX 45
> #PMEGridSizeY 45
> #PMEGridSizeZ 48
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.0
> langevinPistonDecay 50.0
> langevinPistonTemp $temperature
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 100
> reinitvels $temperature
>
> run 8000 ;# 5ps
>
> What can be wrong here? I did not have any errors during psfgn preparation.
>
> Please suggest.
>
> Thanks for any suggestion
>
> Best regards
> Urszula Uciechowska
>
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>

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