Re: well-tempered metadynamics deforms the water box and the system becomes unstable..

From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Wed Oct 21 2020 - 09:59:40 CDT

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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