![\"dia\"](\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/dia.jpg\")
<\/a><\/p>\nDownload a PDF tutorial of running GaMD simulations on alanine dipeptide.<\/a><\/span><\/p>\n Download Source files of the GaMD-Amber tutorial<\/a> (31.8MB zip file)\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>\n Example 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>\n nstlim = 26000000, igamd = 3, iE = 1, irest_gamd = 0, nstlim = 50000000, igamd = 3, iE = 1, irest_gamd = 1, nstlim = 50000000, igamd = 3, iE = 1, irest_gamd = 1, Note: You can also perform multiple independent GaMD simulations with randomized atomic velocities by repeating jobs #2 and #3.<\/span><\/p>\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, <\/p>\n icfe = 1, ifsc = 1, gti_cpu_output = 0, gti_add_sc = 1, ibblig = 1, nlig = 10, atom_p = 2472, atom_l = 4, dblig = 3.7,<\/p>\n OR<\/p>\n igamd = 11, irest_gamd = 0, <\/p>\n icfe = 1, ifsc = 1, gti_cpu_output = 0, gti_add_sc = 1, ibblig = 2, nlig = 10, atom_l = 4, Example input parameters used in Pep-GaMD simulations include the following in addition to those used in conventional MD:<\/p>\n <\/p>\n icfe = 1, ifsc = 1, gti_cpu_output = 0, gti_add_sc = 1, 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> \u00a0 <\/strong>icfe = 1, ifsc = 1, gti_cpu_output = 0,gti_add_sc = 1, 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":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2482","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/users\/22429"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/comments?post=2482"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2482\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2390"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/media?parent=2482"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Job #1: cMD and GaMD equilibration<\/h3>\n
\nirest = 0,
\nntx = 1,<\/strong><\/em><\/p>\n
\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
\nirest = 0,
\nntx = 1,<\/strong><\/em><\/p>\n
\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
\nirest = 1,
\nntx = 5,<\/strong><\/em><\/p>\n
\nntcmd = 0, nteb = 0, ntave = 200000,
\nntcmdprep = 0, ntebprep = 0,
\nsigma0P = 6.0, sigma0D = 6.0,<\/strong><\/em><\/p>\nLiGaMD in Amber<\/h2>\n
\nntcmd = 700000, nteb = 27300000, ntave = 140000,
\nntcmdprep = 280000, ntebprep = 280000,
\nsigma0P = 4.0, sigma0D = 6.0, iEP = 2, iED=1,<\/em><\/strong><\/p>\n
\ntimask1 = ‘:225’, scmask1 = ‘:225’,
\ntimask2 = ”, scmask2 = ”,<\/p>\n
\nntcmd = 700000, nteb = 27300000, ntave = 140000,
\nntcmdprep = 280000, ntebprep = 280000,
\nsigma0P = 4.0, sigma0D = 6.0, iEP = 2, iED=1,<\/em><\/strong><\/p>\n
\ntimask1 = ‘:225’, scmask1 = ‘:225’,
\ntimask2 = ”, scmask2 = ”,<\/p>\n
\nntmsd = 50000, nftau = 10, dblig = 20,<\/p>\nPep-GaMD in Amber<\/h2>\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
\ntimask1 = ‘:225’, scmask1 = ‘:225’,
\ntimask2 = ”, scmask2 = ”,<\/p>\nPPI-GaMD in Amber<\/h2>\n
\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
\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":"