Request for help on error fixing

From: Amir Zeb (zebamir85_at_gmail.com)
Date: Thu Jul 22 2021 - 01:10:49 CDT

Dear NAMD users,

I want to simulate protein-popc complex while applying surface tension to
the membrane only.
I minimized my system for 40,000 steps of minimization. When I subject the
minimized system to simulation without assigning surface tension, it runs
smoothly. But when I apply surface tension (even 5 dyn/cm), the
simulation crashes immediately after the minimization step (let say 5000 or
20000 whatever minimization I use). I tried a number of options e.g.
timestep increase and decrease, Temperature increase and decrease, surface
tension value increase and decrease and several others, but couldn't find
the solution. The error message and confi my config file is given here.
Kindly guide me if possible.

Thanks!

ENERGY: 5000 19885.2122 16807.7101 10747.2198
81.3473 -700796.1791 73517.3579 0.0000 0.0000
136165.4787 -443591.8531 311.4674 -579757.3318
 -444166.6838 311.4674 3188.3368 297.2494
 1420037.6825 3188.3368 297.2494

ERROR: Atom 140395 velocity is -2211.21 -27266.4 25447 (limit is 20000,
atom 2054 of 2872 on patch 45 pe 2)
ERROR: Atom 140403 velocity is 160465 76709.9 -72614.6 (limit is 20000,
atom 2062 of 2872 on patch 45 pe 2)
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
patch 45 pe 2).
ERROR: Atom 143592 velocity is -5558.3 -10113.8 -16964.4 (limit is 20000,
atom 1948 of 2190 on patch 62 pe 7)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
patch 62 pe 7).
ENERGY: 5100 154229.9852 143179.4387 14400.4069
1361.8310 -645727.1251 1769540.7398 0.0000 0.0000
18635435.6060 20072420.8824 42627.0377 1436985.2765
 6399910.8948 871.4869 1050248.7237 482934.9381
 1919091.2003 25085.8492 19233.1721

WRITING COORDINATES TO DCD FILE bmdrc_mscl.dcd AT STEP 5100
FATAL ERROR: Exiting prematurely; see error messages above.
[Partition 0][Node 0] End of program

Configuration file:

# NAMD Config file - autogenerated by NAMDgui plugin
# Author: Amir Zeb, amirzeb_at_bmdrc.org

# input

#set input simulation.namd
#coordinates ${input}.coor
#velocities ${input}.vel
#extendedSystem ${input}.xsc

coordinates minimized.pdb
structure minimized.psf
parameters par_all27_prot_lipid_na.inp
parameters param.prm
paratypecharmm on

# output
set output simul_traj
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 100
xstFreq 100

binaryoutput no
binaryrestart no
outputEnergies 100
restartfreq 1000

fixedAtoms off

# Basic dynamics
exclude scaled1-4
1-4scaling 1
COMmotion no
dielectric 1.0

# Simulation space partitioning
switching on
switchdist 9
cutoff 10
pairlistdist 12

# Multiple timestepping
firsttimestep 0
timestep 0.5
stepspercycle 20
#rigidBonds all
nonbondedFreq 2
fullElectFrequency 2

# Temperature control

set temperature 310
temperature $temperature; # initial temperature
#####################################################################################################
# -------Langevin Dynamics------
langevin on; # do langevin dynamics
langevinDamping 1; # damping coefficient (gamma) of
1/ps
langevinTemp $temperature; # bath temperature

#temperature increment
#reassignTemp 100
#reassignIncr 5
#reassignHold 310
#reassignFreq 1000

# ===============================================

PME on
PMEGridSpacing 1.0
wrapWater on ;# wrap water to central cell
wrapAll on ;# wrap other molecules too
wrapNearest off
margin 10

cellBasisVector1 115.976 0 0
cellBasisVector2 0 114.77 0
cellBasisVector3 0 0 106.685
cellOrigin 1.6169999999999973 -0.0019999999999988916 -10.3205
##################################################################################

useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral
to calcualte pressure and
                                       # has less fluctuation, is needed
for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell yes; # yes for an anisotropic system like membrane
useConstantRatio no; # keeps the ratio of the unit cell in the x-y plane
constant A=B

# with grouppressure, works better, holes still there

LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp $temperature
SurfaceTensionTarget 5.0
ExcludeFromPressure on
ExcludeFromPressureFile except-tension.ref
ExcludeFromPressureCol B
#LangevinHydrogen off ;# don't couple langevin bath to hydrogen

# with langevin piston, works!!! But slower.

# ===============================================
# ===============================================

# ---------Scripting
minimize 5000 ;# lower potential energy for 1000
steps
reinitvels $temperature ;# since minimization zeros velocities
run 5000;

Your cooperation will highly be appreciated!

Kind regards!

Amir

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