07 July 2019 3 10K Report

I think that my complex has been moving out of the 12 A octahedron water box (TIP3PBOX) during the 35 ns simulation in Amber 14, since my RMSD from cpptraj isn't stable, and when I've tried to open the rst7 files in VMD, it looks like part of the complex goes out of the box at many points. I also tried to check this with PYMOL by using the ambpdb command to convert the topology and new restart files back into pdb files and saw in PYMOL that part of the complex also went out of the water box. I'm not sure why this is happening though since I think I set periodic boundary conditions. Are there any parameters in my input files that I should try adjusting?

Here are the settings that I used for my input files:

min.in:

&cntrl imin=1, ntx=1, ntmin=1, maxcyc=50000, ncyc=10000, ntpr=100, ntf=1, ntc=1, ntb=1, cut=10.0 &end

heat.in

&cntrl imin=0, irest=0, ntx=1, ntb=1, cut=10, ntr=1, ntc=2, ntf=2, tempi=0.0, temp0=300.0, ioutfm=1, iwrap=1, ntt=3, gamma_ln=2.0, nstlim=50000, dt=0.002, ntpr=1250, ntwx=1250, ntwr=2500 / Keep protein fixed with weak restraints 100.0 RES 1 208 / END END

equil.in

&cntrl imin=0, irest=1, ntx=5, ntb=2, ntp=1, pres0=1.0, taup=2.0, cut=10, ntr=0, ntc=2, ntf=2, tempi=300.0, temp0=300.0, ntt=3, ioutfm=1, iwrap=1, gamma_ln=2.0, nstlim=50000, dt=0.002, ntpr=1250, ntwx=1250, ntwr=2500, / Keep protein fixed with weak restraints 100.0 RES 1 208 /  &end

prod.in:

NPT production &cntrl imin=0, ntx=5, irest=1, ntpr=1250, ntwr=2500, ntwx=1250, ntf=2, ntc=2, ntb=2, ioutfm=1, iwrap=1, cut=10.0, nstlim=500000, dt=0.002, temp0=300, ntt=3, gamma_ln=2.0, ntp=1, pres0=1.0, taup=2.0, / Keep protein fixed with weak restraints 5.0 RES 1 208 /  &end

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