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Tutorial of using GaMD in Amber
Alanine Dipeptide: Source files of the GaMD-Amber tutorial: amber-gamd-tutorial.tgz (30.2MB) Note: While the NVT ensemble has been used in the tutorial simulations with "ntb=1", the NPT ensemble is generally preferred for running GaMD simulations (especially for the GaMD equilibration) with parameters like "ntb = 2, ntp = 1, barostat = 1". Example input parameters 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 Job #3: repeat running jobs using this input file until end of your GaMD production simulation Note: You can also perform multiple independent GaMD simulations with randomized atomic velocities by repeating jobs #2 and #3.
LiGaMD in Amber
Example input parameters used in dual-boost LiGaMD simulations include the following in addition to those used in conventional MD:
igamd = 11, irest_gamd = 0, Pep-GaMD in Amber
Example input parameters used in Pep-GaMD simulations include the following in addition to those used in conventional MD:
igamd = 15, iE = 1, iEP = 1, iED = 1, irest_gamd = 0, |
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