Tutorial of GaMD in Amber

Alanine Dipeptide:

GaMD Theory

A PDF tutorial of running GaMD simulations on alanine dipeptide: GaMD_Amber-Tutorial.pdf

Source files of the GaMD-Amber tutorial: amber-gamd-tutorial.tgz (30.2MB)

 

Template input files for running GaMD in Amber:

In case you are running GaMD simulation on a computer cluster that imposes wallclock limit for simulation jobs, you may divide your long simulation into multiple jobs, which could include for example job #1 for 2 ns conventional MD (cMD) and 50 ns GaMD equilibration, job #2 for starting GaMD production simulation with radomized atomic velocities, and job #3 for extending GaMD production simulation until the end:

Job #1: cMD and GaMD equilibration
&cntrl
imin = 0,
irest = 0,
ntx = 1,

ioutfm = 1,
nstlim = 26000000,
dt = 0.002,
ntt = 3,
gamma_ln = 5.0,
ig = -1,
tempi = 300.0,
temp0 = 300.0,
ntp = 0,
ntb = 1,
ntc = 2,
ntf = 2,
cut = 12,
ntwr = 500,
ntpr = 50,
ntwx = 50,
ntwe = 50,
iwrap = 1,
ntr = 0,
ntwprt = 3216,

igamd = 3, iE = 1, irest_gamd = 0,
ntcmd = 1000000, nteb = 25000000, ntave = 200000,
ntcmdprep = 200000, ntebprep = 800000,
sigma0P = 6.0, sigma0D = 6.0,

&end

Job #2: start GaMD production simulation
&cntrl
imin = 0,
irest = 0,
ntx = 1,

ioutfm = 1,
nstlim = 50000000,
dt = 0.002,
ntt = 3,
gamma_ln = 5.0,
ig = -1,
tempi = 300.0,
temp0 = 300.0,
ntp = 0,
ntb = 1,
ntc = 2,
ntf = 2,
cut = 12,
ntwr = 500,
ntpr = 50,
ntwx = 50,
ntwe = 50,
iwrap = 1,
ntr = 0,
ntwprt = 3216,

igamd = 3, iE = 1, irest_gamd = 1,
ntcmd = 0, nteb = 0, ntave = 200000,
ntcmdprep = 0, ntebprep = 0,
sigma0P = 6.0, sigma0D = 6.0,

&end

Job #3: repeat running jobs using this input file until end of your GaMD production simulation
&cntrl
imin = 0,
irest = 1,
ntx = 5,

ioutfm = 1,
nstlim = 50000000,
dt = 0.002,
ntt = 3,
gamma_ln = 5.0,
ig = -1,
tempi = 300.0,
temp0 = 300.0,
ntp = 0,
ntb = 1,
ntc = 2,
ntf = 2,
cut = 12,
ntwr = 500,
ntpr = 50,
ntwx = 50,
ntwe = 50,
iwrap = 1,
ntr = 0,
ntwprt = 3216,

igamd = 3, iE = 1, irest_gamd = 1,
ntcmd = 0, nteb = 0, ntave = 200000,
ntcmdprep = 0, ntebprep = 0,
sigma0P = 6.0, sigma0D = 6.0,

&end

Note: You can also perform multiple independent GaMD simulations with randomized atomic velocities by repeating jobs #2 and #3.


Copyright Reserved © Yinglong Miao
Last updated: Tue, November 22, 2016