The structure files for the second turn of simulation

From: yp sun (sunyeping_at_yahoo.com.cn)
Date: Sun Aug 26 2012 - 20:30:04 CDT

Dir Sir,     When we run the real NAMD, we usually should do several turns of pre-balance. In the first turn of prebalance, we use psf file as the structure file. But in the second turn of simulation, I am not sure if we should use the coor file generated in the first turn to replace the psf file as the structure file. I do this in my NAMD but got the error message:   FATAL ERROR: UNABLE TO FIND "PSF" STRING IN PSF FILE RI-10_eq1_o.coor. Could you tell me what does it mean? The content of my conf file RI-10_wb_ionized_eq2.conf is as following:                                 structure          RI-10_eq1_o.coor coordinates        RI-10_wb_ionized.pdb   set temperature    310 set outputname     RI-10_eq2_o   firsttimestep      0     ############################################################# ## SIMULATION PARAMETERS                                   ## #############################################################   # Input paraTypeCharmm     on parameters          par_all27_prot_lipid.inp temperature         $temperature     # Force-Field Parameters exclude             scaled1-4 1-4scaling          1.0 cutoff              12.0 switching           on switchdist          10.0 pairlistdist        14.0     # 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    86.6409   0.0      0.0 cellBasisVector2    0.0       77.0141  0.0 cellBasisVector3    0.0       0        75.0888 cellOrigin          31.625    -36.5377    -3.52252   wrapAll             on     # PME (for full-system periodic electrostatics) PME                 yes PMEGridSpacing      1.0   #manual grid definition #PMEGridSizeX        96 #PMEGridSizeY        81 #PMEGridSizeZ        80     # 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   #Harmonic constrain if {0} { constraints           on consref               RI-10_wb_ionized_constr.pdb conskfile             RI-10_wb_ionized_constr.pdb conskcol              B constraintscaling     10.0 }     # Output outputName          $outputname   restartfreq         500     ;# 500steps = every 1ps dcdfreq             1000                                       Could you tell me what leads to the error?                   Best Regards!       Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:57 CST