awsemmd_script/energy_inFilePattern.data at master · luwei0917/awsemmd_script · GitHub

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# 3d protein simulation

units real

timestep 2

dimension	3

boundary s s s
#boundary p p p

neighbor	10 bin
neigh_modify	delay 5

atom_modify sort 0 0.0

special_bonds fene

atom_style	awsemmd

``bonds

``pair_interactions

``read_data_file

``pair_coeff

thermo 1000


``groups

fix		  ``main_fix
#fix     radialconstraint all spring/rg/cylindrical 0.01 0.0# NULL means use the starting configuration to define the radius, otherwise specify in Angstroms
fix     5 all momentum 1000 linear 1 1 1


###################################################################
# calculate and output collective variables during the simulation #
###################################################################
# output wham.dat, a file with collective variables that can be used to compute pmfs
compute     qw alpha_carbons qwolynes rnative.dat 2 0.15
variable    qw equal c_qw
compute     rg alpha_carbons gyration
variable    rg equal c_rg
compute     qo alpha_carbons qonuchic cutoff 12.0 nativecoords.dat 1.2
variable    qo equal c_qo
compute     tc beta_atoms totalcontacts 6.5 2
variable    tc equal c_tc
variable    step equal step

# f_4 = Total energy computed in the fix backbone
# f_4[i] = {eChain eShake eChi eRama eExcluded eDSSP eP_AP eWater eBurial eHelix eAMH-Go eFrag_Mem eSSB}
variable E_chain equal f_4[1]
variable E_shake equal f_4[2]
variable E_chi equal f_4[3]
variable E_rama equal f_4[4]
variable E_excluded equal f_4[5]
variable E_dssp equal f_4[6]
variable E_pap equal f_4[7]
variable E_water equal f_4[8]
variable E_burial equal f_4[9]
variable E_helix equal f_4[10]
variable E_amhgo equal f_4[11]
variable E_fmem equal f_4[12]
variable E_ssb equal f_4[15]
variable E_vecFM equal f_4[13]
variable E_membrane equal f_4[14]
variable E_bond equal emol
variable E_excl equal epair

variable E_P equal v_E_chain+v_E_shake+v_E_chi+v_E_rama+v_E_excluded+v_E_dssp+v_E_pap+v_E_water+v_E_burial+v_E_helix+v_E_amhgo+v_E_fmem+v_E_vecFM+v_E_membrane+v_E_ssb
variable E_P2 equal v_E_chain+v_E_shake+v_E_chi+v_E_rama+v_E_excluded+v_E_dssp+v_E_pap+v_E_water+v_E_burial+v_E_helix+v_E_amhgo+v_E_membrane+v_E_ssb+v_E_bond+v_E_excl
variable E_K     equal ke
variable E_total equal v_E_P+v_E_K
variable E_PP equal pe

fix energy all print 1000 "${step}, ${E_chain}, ${E_shake}, ${E_chi}, ${E_rama}, ${E_excluded}, ${E_dssp}, ${E_pap}, ${E_water}, ${E_burial}, ${E_helix}, ${E_amhgo}, ${E_fmem}, ${E_vecFM}, ${E_membrane}, ${E_ssb},  ${E_P}, ${E_bond}, ${E_excl}" file initial_energy.dat screen no title "Step, Chain, Shake, Chi, Rama, Excluded, DSSP, P_AP, Water, Burial, Helix, AMH-Go, Frag_Mem, Vec_FM, Membrane, SSB, VTotal, Ebond, Epair"
fix wham all print 1000 "${step},  ${qw}, ${rg},  ${qo}, ${tc}, ${E_P}, ${E_K}, ${E_PP}" file initial_wham.dat screen no title "Step, Qw, Rg, Qo, Tc, Energy, E_K, E_P"


reset_timestep	0
#restart         200000 restart
run		1000

velocity all create 200 RANDOM
fix               1 all nve
fix               2 all langevin 200 200 1000.0 RANDOM
reset_timestep	0
#restart         200000 restart
unfix energy
unfix wham
fix energy all print 1000 "${step}, ${E_chain}, ${E_shake}, ${E_chi}, ${E_rama}, ${E_excluded}, ${E_dssp}, ${E_pap}, ${E_water}, ${E_burial}, ${E_helix}, ${E_amhgo}, ${E_fmem}, ${E_vecFM}, ${E_membrane}, ${E_ssb},  ${E_P}, ${E_bond}, ${E_excl}" file energy.dat screen no title "Step, Chain, Shake, Chi, Rama, Excluded, DSSP, P_AP, Water, Burial, Helix, AMH-Go, Frag_Mem, Vec_FM, Membrane, SSB, VTotal, Ebond, Epair"
fix wham all print 1000 "${step},  ${qw}, ${rg},  ${qo}, ${tc}, ${E_P}, ${E_K}, ${E_PP}" file wham.dat screen no title "Step, Qw, Rg, Qo, Tc, Energy, E_K, E_P"

dump		1 all atom 1000 dump.lammpstrj
dump_modify	1 sort id

run		200000