This page describes how to run pH replica exchange simulation in which each replica is at the same temperature but different pH, the solvent model is implicit solvent. Check here for explicit solvent model.

working directory:/home/zwei/work/MD/BPTI/amber_pH/REX_pH/IM

1. Structure Preparation

2. PH Input File Preparation

3. System Minimization

4. Heating the System

CUDA (GPU): Implementation does not support the use of a cutoff in GB simulations.
Require cut > 999.0d0.

change cut value to 1000 in heat.mdin if you want to run with CUDA.

5. Equilibrating the System

These parts are the same as in constant pH without replica exchange, check here for details.

6. pH Replica Exchange Simulation Setup


"To run replica exchange simulations, we need a groupfile, the -rem and -remlog command-line flags, and the variables nstlim and numexchg in the &cntrl namelist of the input files." (Ref. 1)

6.1 mdin Input File


REM for CpH
icnstph=1, dt=0.002, ioutfm=1, ntxo=2,
nstlim=1000, ig=-1, ntb=0, numexchg=1000,
ntwr=10000, ntwx=1000, irest=1,
cut=1000.0, ntcnstph=5, ntpr=1000,
ntx=5, solvph=2, saltcon=0.1, ntt=3,
ntc=2, ntf=2, gamma_ln=10.0, igb=2,


for i in $(seq 1 14); do mkdir $i; done

for i in $(seq 1 14); do sed "s/solvph=2/solvph=$i/" ph_remd.mdin >./$i/ph_remd.mdin; done

for i in $(seq 1 14) ; do cp 6pti.equil.rst7 ./$i/; done

for i in $(seq 1 14) ; do cp 6pti.cpin ./$i/; done

for i in $(seq 1 14); do echo "# pH $i" >>groupfile; echo "-O -i $i/ph_remd.mdin -p 6pti.parm7 -c $i/6pti.equil.rst7 -cpin $i/6pti.cpin -o $i/6pti.md1.mdout -cpout $i/6pti.md1.cpout -cprestrt $i/6pti.md1.cpin -r $i/6pti.md1.rst7 -inf $i/6pti.md1.mdinfo -rem 4 -remlog rem.md1.log -x $i/" >>groupfile; done

mpirun -np 28(n*14) pmemd.MPI -ng 14 -groupfile groupfile


mpirun -np 14 pmemd.cuda.MPI -ng 14 -groupfile groupfile