From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Mon Oct 19 2020 - 12:36:07 CDT
Hi Giacomo,
Thank you for the quick response and apologies for the delayed response. I
was trying different hill weights as you suggested that I noticed the
hill weights aren't updated as soon as the simulation restarts. More
specifically, I perform well-tempered metadynamics though consecutive
simulations each taking 1 nano second. I expect that the hill weight
reported on the first line of the .hills.traj file to be the same as that
of the last line of .hill.traj file from the previous nanosecond of the
simulation, but I see each nanosecond starts from initial hill weight, i.e.
0.1 kcal/mol. The value of the collective variable is updated appropriately
but the hill weight does not. I tried almost all options on the NAMD user
guide on the metadynamics section to get the hill weight updating but it
didn't work. That might be due to my ignorance as I'm new in metadynamics.
Would that be possible to guide me?
All the best,
Zeynab
On Fri, Oct 16, 2020 at 10:11 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hi Zeynab, assuming a 2 fs time step, you're injecting 0.1 kcal/mol of
> energy every ps. That is okay for short times, but if the collective
> variable is not responding to the bias in an ideal manner, that means up to
> 100 kcal/mol every ns. Too much based on my experience.
>
> Which NAMD tutorial did you follow for setting these parameters? I do not
> think that those numbers are a useful recommendation.
>
> Giacomo
>
> On Fri, Oct 16, 2020 at 4:50 AM zeynab hosseini <
> hosseinizeynab93_at_gmail.com> wrote:
>
>> Dear All,
>>
>> I'm interested in calculating the amino acid (AA) adsorption free energy
>> on the infinite carbon nanotube (CNT) using well-tempered metadynamics
>> (WTMD). I solvated the CNT+AA system in a water box and let the system
>> equilibrated (minimization+NPT+ 6ns NVT). Everything is OK with the
>> standard NVT, but as soon as the WTMD is turned on the water
>> molecules start to expand in the way that the water box deforms and the
>> system becomes unstable. The collective variable is the radial distance of
>> carbon alpha of AA from CNT mass center. I followed the NAMD tutorial to
>> set up the WTMD parameters. Would be thankful if you guide me what is
>> wrong.
>>
>> The NAMD version is 2.13b1. Sometimes, the simulation crashes with the
>> following message too. But playing with the values of "hillWeight" and
>> "width" would remove the error although the water molecules are still
>> expanding:
>> Warning: Low global exclusion count! (9467 vs 10214) System unstable or
>> pairlistdist or cutoff too small.
>>
>> ##############################
>> meta.namd:
>> # NAMD Config file
>> # input
>> coordinates = solvate.pdb
>> structure = solvate.psf
>> outputname = cnt-ser_meta_1
>> 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
>> # output
>> restartfreq 1000 # 1000steps = every 2ps
>> dcdfreq 1000
>> xstFreq 1000
>> outputEnergies 1000
>> outputPressure 1000
>> # Continuing a job from the restart files
>> if {1} {
>> set inputname cnt-ser_NVT_6
>> binCoordinates $inputname.restart.coor
>> binVelocities $inputname.restart.vel # remove the "temperature"
>> entry if you use this!
>> extendedSystem $inputname.restart.xsc
>> }
>> # Basic dynamics
>> exclude scaled1-4
>> 1-4scaling 1
>> # Simulation space partitioning
>> switching on
>> switchdist 10
>> cutoff 12
>> pairlistdist 13.5
>> # Multiple timestepping
>> rigidBonds all
>> firsttimestep 0
>> timestep 1
>> nonbondedFreq 1
>> fullElectFrequency 2
>> stepspercycle 20
>> PME yes
>> PMEGridSpacing 1.0
>> # Temperature control
>> set temperature 310
>> #temperature $temperature
>> langevin on
>> langevinTemp $temperature
>> langevinDamping 1
>> langevinHydrogen no
>> # Pressure Control for NPT Ensemble
>> useFlexibleCell no
>> langevinPiston off
>> #metadynamics
>> colvars on
>> colvarsConfig input.in
>> run 200000
>> ####################################
>> input.in:
>> colvarsTrajFrequency 500
>> colvarsRestartFrequency 1000
>> colvar {
>> name Translocation
>> lowerboundary 4.5
>> upperboundary 30.5
>> width 0.5
>> 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 500
>> dumpFreeEnergyFile yes
>> writeHillsTrajectory on
>> hillwidth 0.5
>> wellTempered on
>> biasTemperature 1550
>> }
>> ############################
>>
>> All the best,
>> Zeynab
>>
>
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