############################################################# ## JOB DESCRIPTION ## ############################################################# # IMD simulation of deca-alanine in vacuum # Constant temperature ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure da.psf coordinates imd_ini.pdb outputName da_imd set temperature 300 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_all27_prot_lipid_cmap.prm temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 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 1/ps langevinTemp $temperature langevinHydrogen no ;# don't couple langevin bath to hydrogens # Output binaryoutput no outputEnergies 100 # Fixed Atoms Constraint (set PDB beta-column to 1) if {1} { fixedAtoms on fixedAtomsFile imdfixedatoms.pdb fixedAtomsCol B } # IMD Settings (can view sim in VMD) if {1} { IMDon on IMDport 3000 ;# port number (enter it in VMD) IMDfreq 1 ;# send every 1 frame IMDwait yes ;# wait for VMD to connect before running? } run 100000