VMD-L Mailing List

From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Fri Aug 12 2016 - 15:21:21 CDT

Hi Josh,

Other research using the same molecule have used forces around these
numbers, so that is where I got started. In my reference file, I set the
protein residues 1-440 as the SMD atoms and set protein residues 1500-1700
fixed. The SMD direction was the vector from the fixed atoms to the SMD
atoms. In the configuration file, I changed the dcd frequency and other
frequencies to 1 and ran a very short simulation. My real simulations will
hopefully use a frequency of 500 and run for somewhere between 1 and 5
nanoseconds. My configuration file looks as follows:

#############################################################
## JOB DESCRIPTION ##
#############################################################

# Constant Force Pulling for fully equilibrated alphaVbeta3
# 0.5 nanoseconds with a force of 10 (about 700 pN)

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure alphaVbeta3_wb.psf
coordinates alphaV_full_equil.pdb
outputName first_fully_equilibrated_alphaV

set temperature 310

# Continuing a job from the restart files
#if {0} {
#set inputname myinput
#binCoordinates $inputname.restart.coor
#binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
#extendedSystem $inputname.xsc
#}

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../par_all27_prot_lipid.inp

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature

# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 200.0 0 0
cellBasisVector2 0 200.0 0
cellBasisVector3 0 0 250.0
cellOrigin -16.3 33.85 38.46
}
wrapWater on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

#PME (for full-system periodic electrostatics)
if {0} {
PME yes
PMEGridSpacing 1.0

#manual grid definition
#PMEGridSizeX 32
#PMEGridSizeY 32
#PMEGridSizeZ 64
#}

# Constant Temperature Control
langevin off ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
}

restartfreq 1 ;# 500steps = every 1ps
dcdfreq 1
xstFreq 1
outputEnergies 1
outputPressure 100

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile first_sim_attempt.ref
fixedAtomsCol B
}

# IMD Settings (can view sim in VMD)
if {0} {
IMDon on
IMDport 3000 ;# port number (enter it in VMD)
IMDfreq 1 ;# send every 1 frame
IMDwait no ;# wait for VMD to connect before running?
}

#############################################################
## EXTRA PARAMETERS ##
#############################################################

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

constantforce yes
consforcefile first_sim_attempt.ref

#############################################################
## EXECUTION SCRIPT ##
#############################################################

#Minimization
if {0} {
minimize 10000
reinitvels $temperature
}

run 250 ;# 0.5ns

On Fri, Aug 12, 2016 at 2:45 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Jack,
>
> Usually, the SMD forces should be high enough to force movement, but not
> high enough that everything else stays still by comparison, especially over
> several timesteps. Odds are you are driving your system far too hard, and
> crashing as a result. What does your NAMD configuration file look like?
>
> -Josh
>
> On 08/12/2016 01:31 PM, Jackson Cavett wrote:
> Hello All,
>
> I have been trying to equilibrate and minimize integrin alphaVbeta3 in a
> waterbox. I finished up a long equilibration simulation (about 40 ns), but
> am running into the "ERROR: Constraint failure in RATTLE algorithm for atom
> 994!" when I try to run a constant-force simulation. After reading up on
> this error, I changed the dcd frequency to every timestep and looked at the
> dcd file in VMD. When looking at the dcd file, it looks as though the smd
> atoms being pulled (by about 700 pN) move while every other atom stays
> fixed. It seems to me (though I am far from an expert) that the energy has
> not reached a constant value and therefore I would need more minimization
> steps. Before the equilibration, I minimized the system with three
> different minimzation simulations which were 10,000 timesteps each. My
> system has about 170,000 atoms, which is very large. Would anyone know how
> many minimization steps this system would need? Also, I could be on the
> wrong track with what my problem is, so if anyone has any other ideas that
> would be great. Thank you all for your help!
>
> Thanks,
>
> Jack
>
>