– accelMDG < Is Gaussian accelerated MD on? >
\nAcceptable Values: on or off
\nDefault Value: off
\nDescription: Specifies whether Gaussian accelerated MD (GaMD) is on.<\/p>\n
– accelMDGiE < Flag to set the threshold energy for adding boost potential >
\nAcceptable Values: 1, 2
\nDefault Value: 1
\nDescription: Specifies how the threshold energy is set in GaMD. A value of 1 indicates that the threshold energy is set to its lower bound E = Vmax. A value of 2 indicates that the threshold energy is set to its upper bound E = Vmin + (Vmax – Vmin) \/ k0.<\/p>\n
– accelMDGcMDPrepSteps < no. of preparatory cMD steps >
\nAcceptable Values: Zero or Positive integer
\nDefault Values: 200,000
\nDescription: The number of preparatory conventional MD (cMD) steps in GaMD. This value should be smaller than accelMDGcMDSteps (see below). Potential energies are not collected for calculating the values of Vmax, Vmin, Vavg, \u03c3V during the first accelMDGcMDPrepSteps.<\/p>\n
– accelMDGcMDSteps < no. of total cMD steps in GaMD >
\nAcceptable Values: Positive integer
\nDefault Value: 1,000,000
\nDescription: The number of total cMD steps in GaMD. With accelMDGcMDPrepSteps < t < accelMDGcMDSteps, Vmax, Vmin, Vavg, \u03c3V are collected and at t = accelMDGcMDSteps, E and k0 are computed.<\/p>\n
– accelMDGEquiPrepSteps < no. of preparatory equilibration steps in GaMD >
\nAcceptable Values: Zero or Positive integer
\nDefault Value: 200,000
\nDescription: The number of preparatory equilibration steps in GaMD. This value should be smaller than accelMDGEquiSteps (see below). With accelMDGcMDSteps < t < accelMDGEquiPrepSteps+accelMDGcMDSteps, GaMD boost potential is applied according to E and k0 obtained at t=accelMDGcMDSteps.<\/p>\n
– accelMDGEquiSteps < no. of total equilibration steps in GaMD >
\nAcceptable Values: Zero or Positive integer
\nDefault Value: 1,000,000
\nDescription: The number of total equilibration steps in GaMD. With accelMDGEquiPrepSteps+accelMDGcMDSteps < t < accelMDGEquiSteps +accelMDGcMDSteps, GaMD boost potential is applied, and E and k0 are updated every step.<\/p>\n
– accelMDGSigma0P < upper limit of the standard deviation of the total boost potential in GaMD >
\nAcceptable Values: Positive real number
\nDefault Value: 6.0 (kcal\/mol)
\nDescription: Specifies the upper limit of the standard deviation of the total boost potential. This option is only available when accelMDdihe is off or when accelMDdual is on.<\/p>\n
– accelMDGSigma0D < upper limit of S.D. of the dihedral potential boost in GaMD >
\nAcceptable Values: Positive real number
\nDefault Value: 6.0 (kcal\/mol)
\nDescription: Specifies the upper limit of the standard deviation of the dihedral boost potential. This option is only available when accelMDdihe or accelMDdual is on.<\/p>\n
– accelMDGRestart < Flag to restart GaMD simulation >
\nAcceptable Values: on or off
\nDefault Value: off
\nDescription: Specifies whether the current GaMD simulation is the continuation of a previous run. If this option is turned on, the GaMD restart file specified by accelMDGRestartFile (see below) will be read.<\/p>\n
– accelMDGRestartFile < Name of GaMD restart file >
\nAcceptable Values: UNIX filename
\nDescription: A GaMD restart file that stores the current number of steps, maximum, minimum, average, standard deviation of the dihedral and\/or total potential energies (depending on the accelMDdihe and accelMDdual parameters) and the current timestep settings. This file is saved automatically every restartfreq steps. If accelMDGRestart is turned on, this file will be read and the simulation will restart from the point where the file was written.<\/p>\n
NOTE: Suitable parameters from aMD, including “accelMD”, “accelMDdihe”, “accelMDdual”, “accelMDFirstStep”, “accelMDLastStep” and “accelMDOutFreq”, are shared by GaMD. Please refer to the NAMD user manual for their detailed description.<\/p>\n","protected":false},"excerpt":{"rendered":"
Simulation Parameter Settings – accelMDG < Is Gaussian accelerated MD on? > Acceptable Values: on or off Default Value: off Description: Specifies whether Gaussian accelerated MD (GaMD) is on. – accelMDGiE < Flag to set the threshold energy for adding boost potential > Acceptable Values: 1, 2 Default Value: 1 Description: Specifies how the threshold … Read more<\/a><\/p>\n","protected":false},"author":22429,"featured_media":0,"parent":2390,"menu_order":8,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2452","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\/2452","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=2452"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2452\/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=2452"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}