Tutorial of GaMD in Amber
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)
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:
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
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. |

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