From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jul 14 2022 - 08:57:19 CDT
Packmol is very useful but not really perfect at achieving a good initial
density.
If you're far from the equilibrium density for that pressure, try running
multiple short jobs with margin, so that NAMD will re-initialize the patch
grid every time from the new simulation cell.
Also, the parameters below will make for a rather fast/noisy feedback from
the barostat. Try increasing them to make the equilibration a little
slower but more stable.
langevinPistonPeriod 50.0
langevinPistonDecay 25.0
On Thu, Jul 14, 2022 at 9:51 AM Nur Afiqah Ahmad <
nur_afiqah.ahmad_at_unsw.edu.au> wrote:
> My simulation box is 30x30x30. I make it using packmol before generating
> the psf file.
>
> Get Outlook for iOS
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> ------------------------------
> *From:* Vermaas, Josh <vermaasj_at_msu.edu>
> *Sent:* Thursday, July 14, 2022 11:39:39 PM
> *To:* namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Nur Afiqah Ahmad <
> nur_afiqah.ahmad_at_unsw.edu.au>
> *Subject:* Re: namd-l: Error
>
>
> How big is your simulation box, and how was it made? Usually, the problem
> is a box that is either too big (unlikely for a 30x30x30 box), too small,
> or doesn’t have enough atoms in it to maintain something close to the
> original density.
>
>
>
> -Josh
>
>
>
> *From: *<owner-namd-l_at_ks.uiuc.edu> on behalf of Nur Afiqah Ahmad <
> nur_afiqah.ahmad_at_unsw.edu.au>
> *Reply-To: *"namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, Nur Afiqah Ahmad <
> nur_afiqah.ahmad_at_unsw.edu.au>
> *Date: *Thursday, July 14, 2022 at 9:33 AM
> *To: *"namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> *Subject: *namd-l: Error
>
>
>
> Hai, I want to do an FEP calculation for methane in octanol solution.
> However, I’m getting an error while running the equilibration step. Here is
> the error.
>
>
>
> Reason: FATAL ERROR: Periodic cell has become too small for the original
> patch grid! Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid
> simulation.
>
>
>
> I’m already trying the solution from the previous list which tries to
> restart the simulation from the previous checkpoint and by increasing the
> margin but it doesn't work. Can anyone help me to solve the problem?
> Attach here also my configuration file.
>
>
>
> #############################################################
>
> ## JOB DESCRIPTION ##
>
> #############################################################
>
>
>
> # Minimize followed by Production Run
>
>
>
> structure mixture.psf
>
> coordinates mixture.pdb
>
>
>
> set temperature 300 ;# target temperature used several times below
>
>
>
> # starting from scratch
>
> temperature $temperature ;# initialize velocities randomly
>
>
>
> outputName eq ;# base name for output from this run
>
>
>
> restartfreq 5000 ;# 1000 steps = every 1ps
>
> dcdfreq 5000
>
>
>
> outputEnergies 5000 ;# 100 steps = every 0.2 ps
>
> outputpressure 5000
>
> XSTFreq 5000
>
>
>
> # Force-Field Parameters
>
> paraTypeCharmm on
>
> parameters ../toppar/par_all36_cgenff.prm
>
> parameters ../toppar/par_all36_carb.prm
>
> parameters ../toppar/par_all36_lipid.prm
>
> parameters ../toppar/par_all36_na.prm
>
> parameters ../toppar/par_all36_prot.prm
>
> parameters ../toppar/par_all36m_prot.prm
>
> parameters toppar_methane.str
>
> parameters ../toppar/toppar_water_ions_namd.str
>
>
>
> # system dimensions
>
> cellBasisVector1 30.000 0.000 0.000
>
> cellBasisVector2 0.000 30.000 0.000
>
> cellBasisVector3 0.000 0.000 30.000
>
> cellOrigin -0.17385032773017883 -0.10125097632408142
> -0.045012082904577255
>
>
>
> wrapAll on
>
> wrapWater on
>
>
>
> # PME (for full-system periodic electrostatics)
>
> PME yes
>
> PMEGridSpacing 1.0
>
>
>
> # These are specified by CHARMM
>
> exclude scaled1-4 # non-bonded exclusion policy
> to use "none,1-2,1-3,1-4,or scaled1-4"
>
> 1-4scaling 1.0
>
> switching on
>
> vdwForceSwitching yes; # New option for force-based
> switching of vdW
>
> cutoff 13.5; # may use smaller, maybe 10.,
> with PME
>
> switchdist 10.0; # cutoff - 2.
>
> pairlistdist 16.0; # stores the all the pairs
> with in the distance it should be larger
>
> stepspercycle 20; # 20 redo pairlists every ten
> steps
>
> pairlistsPerCycle 2; # 2 is the default
>
> Margin 4.0;
>
>
>
> # CONSTRAINTS
>
> #fixedAtoms on
>
> #fixedAtomsFile freeze.fep
>
> #fixedAtomsCol B
>
> #fixedAtomsForces on
>
>
>
> # Integrator Parameters
>
> timestep 2.0 ;# 2fs/step
>
> rigidBonds all ;# needed for 2fs steps
>
> nonbondedFreq 1 ;# nonbonded forces every step
>
> fullElectFrequency 2 ;# PME only every other step
>
>
>
> # Constant Temperature Control
>
> langevin on ;# langevin dynamics
>
> langevinDamping 1.0 ;# damping coefficient of 1/ps
>
> langevinTemp $temperature ;# random noise at this level
>
>
>
> # Constant Pressure Control (variable volume)
>
> useGroupPressure yes ;# needed for rigidBonds
>
> useFlexibleCell no
>
> useConstantArea no
>
>
>
> langevinPiston on
>
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>
> langevinPistonPeriod 50.0
>
> langevinPistonDecay 25.0
>
> langevinPistonTemp $temperature
>
>
>
> # Colvars can be used to restrain movement of the center of mass
>
> #colvars on
>
> #colvarsConfig fixoctdistance20.in
>
>
>
> #############################################################
>
> ## EXECUTION SCRIPT ##
>
> #############################################################
>
>
>
> minimize 1000
>
> run 5000000 ;# 5ns
>
>
>
> exit
>
>
>
>
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