Difference between revisions of "Running GMIN with MD move steps AMBER"
import>Mp466 |
import>Mp466 |
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<b>saltcon=0.2</b> sets the surrounding (monovalent) salt concentration to 0.2 [mol/L]. <b>temp1 = 1</b> sets |
<b>saltcon=0.2</b> sets the surrounding (monovalent) salt concentration to 0.2 [mol/L]. <b>temp1 = 1</b> sets |
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the initial temperature in Kelvin <b>temp0 = 1</b> sets the rest of the final temperature in Kelvin. |
the initial temperature in Kelvin <b>temp0 = 1</b> sets the rest of the final temperature in Kelvin. |
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The langevin thermostat is set by <b>ntt=3</b> and the collision rate of 100 ps-1 is set by <b>gamma_ln=100</b> |
The langevin thermostat is set by <b>ntt=3</b> and the collision rate of 100 ps-1 is set by <b>gamma_ln=100</b> |
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+ | .5ps of MD with a 1.0fs time step is set by<b>nstlim=500, dt=0.001</b> |
Revision as of 14:38, 28 July 2009
Running GMIN with AMBER with MD move steps can be more efficient than with random cartesian move steps. To do so one needs the GMIN input file data, the AMBER file min.in for defining the energy function used whilst minimising, and the AMBER file min_md.inf or defining the energy function, parametrs for the MD move steps. The amber coordinate and topology files are also necessary, but will not be delt with here. These files are approximate.
GMIN input data file
SLOPPYCONV 1.0D-2 TIGHTCONV 1.0D-3 UPDATES 8000 MAXERISE 0.001 STEPS 100 1.0 STEP 0.00 0.0 AMBER9 coords.inpcrd inpcrd AMBERMDSTEPS MAXIT 10000 10000 MAXBFGS 1.0 TEMPERATURE 1.0 RADIUS 300.0 DUMPSTRUCTURES
GMIN AMBER minimisation min.in file
# Minimisation Parameters &cntrl imin = 1, ncyc = 1, maxcyc = 1, igb = 2, saltcon=0.2, ntb = 0, cut = 999.0, rgbmax = 25.0, /
For the minimisation, imin = 1, and no cutoffs cut = 999.0 should be used. Also igb=2 means that we are using the 2nd GB models is expected to perform well on proteins. saltcon=0.2 sets the surrounding (monovalent) salt concentration to 0.2 [mol/L]. ncyc = 1 perform 1 cycle of minimisation maxcyc = 1 perform 1 a maximum number of minimisation steps.
GMIN AMBER input min_md.in file
# MD Paramaters &cntrl imin = 0, tempi = 700.0, temp0 = 700.0, ntt = 3, gamma_ln = 1.0, nstlim = 500, dt = 0.001, igb = 2, saltcon = 0.2, ntb = 0, ntpr = 350, ntwx = 10,nrespa=1, cut = 999.0, rgbmax=8.22, /
For the MD steps, imin=0, no minisations are performed. and no cutoffs cut = 999.0 should be used. Also igb=2 means that we are using the 2nd GB models is expected to perform well on proteins. saltcon=0.2 sets the surrounding (monovalent) salt concentration to 0.2 [mol/L]. temp1 = 1 sets the initial temperature in Kelvin temp0 = 1 sets the rest of the final temperature in Kelvin.
The langevin thermostat is set by ntt=3 and the collision rate of 100 ps-1 is set by gamma_ln=100
.5ps of MD with a 1.0fs time step is set bynstlim=500, dt=0.001