\u00a0<\/span><\/p>\n\u00a0Note: 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”.<\/strong><\/p>\nExample input parameters for running GaMD in Amber: <\/strong><\/p>\n 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:<\/span><\/p>\nJob #1: cMD and GaMD equilibration<\/h3>\n
nstlim = 26000000,
\nirest = 0,
\nntx = 1,<\/strong><\/em><\/p>\nigamd = 3, iE = 1, irest_gamd = 0,
\nntcmd = 1000000, nteb = 25000000, ntave = 200000,
\nntcmdprep = 200000, ntebprep = 800000,
\nsigma0P = 6.0, sigma0D = 6.0, <\/em><\/strong><\/p>\nJob #2: start GaMD production simulation<\/h3>\n
nstlim = 50000000,
\nirest = 0,
\nntx = 1,<\/strong><\/em><\/p>\nigamd = 3, iE = 1, irest_gamd = 1,
\nntcmd = 0, nteb = 0, ntave = 200000,
\nntcmdprep = 0, ntebprep = 0,
\nsigma0P = 6.0, sigma0D = 6.0,<\/strong><\/em><\/p>\nJob #3: repeat running jobs using this input file until end of your GaMD production simulation<\/h3>\n
nstlim = 50000000,
\nirest = 1,
\nntx = 5,<\/strong><\/em><\/p>\nigamd = 3, iE = 1, irest_gamd = 1,
\nntcmd = 0, nteb = 0, ntave = 200000,
\nntcmdprep = 0, ntebprep = 0,
\nsigma0P = 6.0, sigma0D = 6.0,<\/strong><\/em><\/p>\nNote: You can also perform multiple independent GaMD simulations with randomized atomic velocities by repeating jobs #2 and #3.<\/span><\/p>\nLiGaMD in Amber<\/h2>\n
Example input parameters used in dual-boost LiGaMD simulations include the following in addition to those used in conventional MD:<\/p>\n
igamd = 11, irest_gamd = 0,
\nntcmd = 700000, nteb = 27300000, ntave = 140000,
\nntcmdprep = 280000, ntebprep = 280000,
\nsigma0P = 4.0, sigma0D = 6.0, iEP = 2, iED=1,<\/em><\/strong><\/p>\n <\/p>\n
icfe = 1, ifsc = 1, gti_cpu_output = 0, gti_add_sc = 1,
\ntimask1 = ‘:225’, scmask1 = ‘:225’,
\ntimask2 = ”, scmask2 = ”,<\/p>\n
ibblig = 1, nlig = 10, atom_p = 2472, atom_l = 4, dblig = 3.7,<\/p>\n
OR<\/p>\n
igamd = 11, irest_gamd = 0,
\nntcmd = 700000, nteb = 27300000, ntave = 140000,
\nntcmdprep = 280000, ntebprep = 280000,
\nsigma0P = 4.0, sigma0D = 6.0, iEP = 2, iED=1,<\/em><\/strong><\/p>\n <\/p>\n
icfe = 1, ifsc = 1, gti_cpu_output = 0, gti_add_sc = 1,
\ntimask1 = ‘:225’, scmask1 = ‘:225’,
\ntimask2 = ”, scmask2 = ”,<\/p>\n
ibblig = 2, nlig = 10, atom_l = 4,
\nntmsd = 50000, nftau = 10, dblig = 20,<\/p>\n
Pep-GaMD in Amber<\/h2>\n
Example input parameters used in Pep-GaMD simulations include the following in addition to those used in conventional MD:<\/p>\n
\nigamd = 15, iE = 1, iEP = 1, iED = 1, irest_gamd = 0,
\nntcmd = 1000000, nteb = 1000000, ntave = 50000,
\nntcmdprep = 200000, ntebprep = 200000,
\nsigma0P = 6.0, sigma0D = 6.0,<\/em><\/strong><\/p>\n <\/p>\n
icfe = 1, ifsc = 1, gti_cpu_output = 0, gti_add_sc = 1,
\ntimask1 = ‘:225’, scmask1 = ‘:225’,
\ntimask2 = ”, scmask2 = ”,<\/p>\n
PPI-GaMD in Amber<\/h2>\n
Example input parameters used in PPI-GaMD_Dual simulations include the following in addition to those used in conventional MD:<\/p>\n
\u00a0 igamd = 17, iEP = 2, iED = 1, irest_gamd = 0,<\/strong>
\n\u00a0 ntcmd = 1000000, nteb = 1000000, ntave = 50000,<\/strong>
\n\u00a0 ntcmdprep = 200000, ntebprep = 200000,<\/strong>
\n\u00a0 sigma0P = 6.0, sigma0D = 6.0,<\/strong><\/p>\n\u00a0 <\/strong>icfe = 1, ifsc = 1, gti_cpu_output = 0,gti_add_sc = 1,
\n\u00a0 <\/strong>timask1 = ‘:1-110’, scmask1 = ‘:1-110’,
\n\u00a0 <\/strong>timask2 = ”, scmask2 = ”,
\n\u00a0 <\/strong>bgpro2atm=1, edpro2atm=1453,<\/p>\n","protected":false},"excerpt":{"rendered":"Alanine Dipeptide Download a PDF tutorial of running GaMD simulations on alanine dipeptide. Download Source files of the GaMD-Amber tutorial (31.8MB zip file)\u00a0 \u00a0Note: 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 … Read more<\/a><\/p>\n","protected":false},"author":22429,"featured_media":0,"parent":2390,"menu_order":6,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2482","page","type-page","status-publish","hentry","odd"],"acf":[],"yoast_head":"\nGaMD-Amber: Tutorial - Miao Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/gamd\/tutorial\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"GaMD-Amber: Tutorial - Miao Lab\" \/>\n<meta property=\"og:description\" content=\"Alanine Dipeptide Download a PDF tutorial of running GaMD simulations on alanine dipeptide. 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![\"dia\"](\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/dia.jpg\")
<\/a><\/p>\n