From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Oct 21 2020 - 10:26:15 CDT
Hi Zeynab, the bias isn't correctly restarted because there is no command
in there to load the state file.
Quite simply, that tutorial shows how to do a quick metadynamics run for
demonstration purposes, so it did not provide you with instructions on how
to restart it. You can find these here:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cv_command_loadsave
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvars_mdengine_params
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvars_input
and pretty much it boils down to using either "colvarsInput" or "cv load
..." in the NAMD script to give restart information to Colvars.
This information is a bit harder to find in the NAMD manual, because the
entire Colvars doc is crammed into one section of the NAMD manual. Also,
in the NAMD website the links to the same sections are not consistent
between NAMD versions, which throws off the search engines when searching
the mailing list archives. For this reason, using the Colvars doc page
linked above or the PDF version
<https://colvars.github.io/pdf/colvars-refman-namd.pdf> would be more
appropriate.
Giacomo
On Wed, Oct 21, 2020 at 11:03 AM zeynab hosseini <hosseinizeynab93_at_gmail.com>
wrote:
> Hi Giacomo,
>
> *>>>>Can you give some details about how you are restarting the
> simulation? E.g. did you use either the NAMD keyword/command colvarsInput
> or the "cv load ..." command?*
> *>>>>I tested the Colvars versions bundled with the latest NAMD major
> versions: 2.12, 2.13 and 2.14. 2.12 and 2.13 include a minor bug (see here
> <https://github.com/Colvars/colvars/pull/357> for the detailed fix), which
> adds a new Gaussian at the first step, which coincides with the last step
> of the previous run, if you are restarting. In your case, that would mean
> an extra Gaussian hill every 1 ns. NAMD 2.14 will instead wait for a
> "true" new step when restarting.*
>
> Thank you for the prompt reply and your time. I used both 2.13b2 and 2014
> versions of NAMD and for both cases the hill weights aren't properly
> restarted. I didn't use the "cv load command". I just followed the
> metadynamics tutorial on the NAMD page (link is as follows), creating a
> collective variable input file which is called from within the namd
> configuration file, containing the collective variable info and the
> metadynamics commands.
>
> NAMD tutorial:
>
> https://www.ks.uiuc.edu/Training/Tutorials/namd/metadynamics-tutorial/meta-tutorial.pdf
>
> *>>>> Those plots suggest that either there is a bug that is triggered by
> specific ways of restarting (hence my asking), or there is no restart
> information given to the metadynamics code and it always starts over again
> every ns.*
>
> I put here the namd configuration and input files contents so that you
> have a look if possible:
> Namd configuration file:
> #####################
> structure solvate.psf
> coordinates solvate.pdb
> outputName cnt-ser_meta_2
>
> set temperature 310
>
> # Continuing a job from the restart files
> if {1} {
> set inputname cnt-ser_meta_1
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel ;# remove the "temperature"
> entry if you use this!
> extendedSystem $inputname.restart.xsc
> }
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters toppar_c36_jul20/par_all36_prot.prm
> mergeCrossterms yes
> parameters toppar_c36_jul20/par_all36_lipid.prm
> parameters toppar_c36_jul20/par_all36_carb.prm
> parameters toppar_c36_jul20/par_all36_na.prm
> parameters toppar_c36_jul20/par_all36_cgenff.prm
> parameters toppar_c36_jul20/toppar_water_ions-cmt.str
>
> wrapWater on
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
> COMmotion no
> zeromomentum no
>
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> PMEGridSpacing 1.0
> }
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
>
> restartfreq 1000 ;# 1000steps = every 2ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 1000
> outputPressure 1000
>
> #metadynamics
> colvars on
> colvarsConfig input.in
>
> run 500000 ;# 1 ns
> #############################
>
>
> input.in file:
> #############
> colvarsTrajFrequency 500
> colvarsRestartFrequency 1000
>
> colvar {
> name Translocation
>
> upperboundary 30.5
> lowerboundary 4.0
> upperWallConstant 100.0
> lowerWallConstant 100.0
> width 0.02
>
> distanceXY {
> main {
> atomnumbers { 165 }
> }
> ref {
> atomnumbers {
> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
> 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53
> 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78
> 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102
> 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121
> 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140
> 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
> 160
> }
> }
> axis ( 0.0, 0.0, 1.0 )
> }
> }
>
>
> metadynamics {
> name meta-distance
> colvars Translocation
> hillWeight 0.1
> newHillFrequency 250
> dumpFreeEnergyFile yes
> writeHillsTrajectory on
> hillwidth 0.2
> wellTempered on
> # bias factor=2
> biasTemperature 310
> }
> #######################
>
> Thanks in advance for your help,
> All the best,
> Zeynab
>
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