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Amber 10 Tutorial. Prebath and Equilibriation. Amber10 manual. all page numbers in this power point refer to the “Amber10 manual.pdf” The reason for a prebath is that amber recommends heating the system up to your target temperature before pressure coupling it. bathi.sh.
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Amber 10 Tutorial Prebath and Equilibriation
Amber10 manual • all page numbers in this power point refer to the “Amber10 manual.pdf” • The reason for a prebath is that amber recommends heating the system up to your target temperature before pressure coupling it.
bathi.sh The code below is the code to run a prebath in sander. It will be described in detail in the next few slides. • #Running initial bath before equilibriation for bnr w/ H20 • cat << EOF > bathi.in • #prebath for bnr, explicit solvation • &cntrl • nstlim=20000,dt=0.001,ntwx=100,ntwv=100,ntwe=1, • ntt=1,ntb=1,temp0=300,tempi=300,tautp=1.0, • cut=12.0,igb=0,imin=0,ntx=1,irest=0, • / • EOF • echo 'begin bnrprebath' >> timer.dat • date >> timer.dat • bnra=/home/saguaro/Quickgo/amber10tutorial • sander -ibathi.in -o bathi.out -p $bnra/bnrwh2o.top -c $bnra/minimize/min.rst -r bathi.rst -e bathi.ene -x bathi.traj -v bathi.vel • date >> timer.dat • echo 'end bnrprebath' >> timer.dat
bathi.in • nstlim = 20000 pg 28 • 20000 md steps will be preformed • ntwx,ntwv,ntwe = # pg 25,26 • these denote the number (#) of steps between writing the positions (x), velocities (v), or energies (e) of the run. • ntt = 1 pg 29 • 1 is a weak-coupling algorithm for temperature coupling. This scales the velocities of all atoms with a single scaling constant. This is non-canonical and is similar to iTC=2 in saguaro (Berdensen). • dt = 0.001 • time step used in the md run. This is in picoseconds. • ntb = 1 pg 35 • 1 means constant volume periodic boundary conditions. • This is the same as iPBC in saguaro • temp0 = 300 pg 30 • target and reference temperature at which the system should be kept. This is in units of Kalvin.
bathi.in • tempi = 300 pg 30 • initial temperature of the run if ntx < 0. This is set via a maxwellian distribution. • tautp = 1.0 pg 30 • time constant for temperature coupling. similar to TAUT in saguaro. • cut = 12.0 pg 35 • non-bonded cutoff in angstroms. • igb = 0 pg 36 & 54 • 0 means do not use generalized born model, this is slightly similar to iGB in saguaro • imin = 0 pg 23 • 0 no minimization and only molecular dynamics. • ntx = 1 pg 24 • read in formatted (not binary) coordinate file without velocities. • irest = 0 pg 24 • 0 means this is not a restart run. 1 is a restart run. This couples to ntx.
equilibriation The next slides refer to the equilibriation run which uses the previous set temperature from the prebath: • #Running equilibriation for bnr w/ H20 • cat << EOF > eq.in • #20000 step equilibriation, explicit solvation • &cntrl • nstlim=20000,dt=0.001,ntwx=100,ntwv=100,ntwe=1, • ntt=1,ntb=2,temp0=300,tempi=300,tautp=1.0, • cut=8.0,igb=0,imin=0,ntx=5,irest=1,ntp=1, • pres0=1.0,taup=1.0, • / • EOF • echo 'begin bnrequilibriation' >> timer.dat • date >> timer.dat • bnra=/home/saguaro/Quickgo/amber10tutorial • sander -ieq.in -o min.out -p $bnra/bnrwh2o.top -c ./bathi.rst -r eq.rst -e eq.ene -x eq.traj -v eq.vel • date >> timer.dat • echo 'end bnrequilibriation' >> timer.dat
eq.in • ntb = 2 pg 35 • periodic boundary contition, constant pressure • cut = 8.0 pg 35 • non-bonded cutoff in angstroms. changed to 8 to hopefully speed up the PME method. • ntx = 5 pg 24 • both positions and velocities are read in from the coordinate file, formatted (not binary). This is for a restart run irest=1. • irest = 1 pg 24 • 1 means this run is a restart from a previous run. The positions and velocities are read in from the coordinate file and the initial temperature is set by the initial velocities. • ntp = 1 pg 31 • 1 means isotropic lattice vectory scaling for pressure coupling • pres0 = 1.0 pg 31 • This is the desired pressure to scale the run to. Units are in bars. i.e. atmosphere. • taup = 1.0 pg 31 • This is the pressure scaling time constant. A higher/lower time will make the pressure scale slower/faster.
Prebath and Equilibriation • Examples of both of these runs can be found on saguaro@dnaseq:~/Quickgo/amber10tutorial/bnrMD/equilibriate/ • The Prebath has the prefix bathi. • The Equilibriation has the prefix eq.
