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create_project_in_crystal_template.in
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# 3d protein simulation
units real
timestep 5
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
bond_style harmonic
pair_style vexcluded 2 3.5 3.5
read_data data.crystal
# read_restart restart.unfolded
pair_coeff * * 0.0
pair_coeff 1 1 20.0 3.5 4.5
pair_coeff 1 4 20.0 3.5 4.5
pair_coeff 4 4 20.0 3.5 4.5
pair_coeff 3 3 20.0 3.5 3.5
group alpha_carbons id ALPHA_CARBONS
group beta_atoms id BETA_ATOMS
group oxygens id OXYGENS
# group n_end id 1 2 3
# group c_end id 541 542 543
thermo 1000
# fix radialconstraint all spring/rg/cylindricalZdependent 0.1 0.0 0.2 30# NULL means use the starting configuration to define the radius, otherwise specify in Angstroms
fix 4 alpha_carbons backbone beta_atoms oxygens fix_backbone_coeff.data crystal.seq
variable step equal step
###################################################################
# 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 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[13]
variable E_vecFM equal f_4[15]
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+v_E_bond+v_E_excl
variable E_P3 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
fix 1 all nve
fix 2 all langevin 800 800 10000.0 RANDOM
dump 1 all atom 1000 NUMBER/dump.lammpstrj
dump 2 all custom 1000 NUMBER/dump.unwraped id type xsu ysu zsu
dump_modify 1 sort id
fix energy all print 1000 "${step}, ${E_chain}, ${E_chi}, ${E_rama}, ${E_water}, ${E_helix}, ${E_amhgo}, ${E_fmem}, ${E_membrane}, ${E_P3}, ${E_bond}, ${E_excl}" file NUMBER/energy.dat screen no title "Steps, Chain, Chi, Rama, Water, Helix, AMH-Go, Frag_Mem, Membrane, VTotal, Ebond, Epair"
fix wham all print 1000 "${step}, ${qw}, ${rg}, ${tc}, ${E_P3}" file NUMBER/wham.dat screen no title "Steps, Qw, Rg, Tc, Energy"
restart 100000 restart
run 100000
unfix 2
fix 2 all langevin 800 300 10000.0 RANDOM
# reset_timestep 0
run 800000