Re: Error

From: Nur Afiqah Ahmad (nur_afiqah.ahmad_at_unsw.edu.au)
Date: Thu Jul 14 2022 - 08:46:56 CDT

My simulation box is 30x30x30. I make it using packmol before generating the psf file.

Get Outlook for iOS<https://urldefense.com/v3/__https://aka.ms/o0ukef__;!!DZ3fjg!9JdpGafxdVsk82pOWkBoXdrpr6roGEO1VnynvbOeNMBG97MDpf0c_PjdLY3dCwG0elaCy8gBdCAld8BHXltuC8AztLKhDdAO7g$ >
________________________________
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 doesnít 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, Iím 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.

Iím 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

This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST