From: shreya bhattacharya (shreya199713_at_gmail.com)
Date: Thu Jul 14 2022 - 08:53:40 CDT
Oh, then your box size that you defined must be smaller than your actual
system size. Try to increase your periodic box size based on how big is
your system .
On Thu, Jul 14, 2022, 7:21 PM 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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