1
$\begingroup$

I'm minimizing the energy of a protein with NAMD using the fixedatom feature. I put my protein in a water box, and I allow all atoms other than the protein backbone to be unconstrained. After running the minimization, I used VMD's NAMD Plot for NAMD's log file and the TOTAL3 total energy option, which resulted in some energy peaks that weren't present until this step:

enter image description here

Are those peaks normal to have? If not, what causes them?

Here is the NAMD log file. The NAMD configuration file used for the minimization is:

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

# Minimization and Equilibration of 
# Human Pi GST in a Water Box
# N, V, E simulation


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

structure          ionized.psf
coordinates        ionized_h_free_min.pdb

set temperature    310

firsttimestep      0

# output
set output              Cry1_side_free
outputname              $output
dcdfile                 ${output}.dcd
xstFile                 ${output}.xst
dcdfreq                 50
xstFreq                 50

binaryoutput            no
binaryrestart           no
outputEnergies          100
restartfreq             1000

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

# Input
paraTypeCharmm      on
parameters          /usr/local/lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/par_all27_prot_lipid_na.inp 
temperature         $temperature


# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        14.0


# Integrator Parameters
timestep            1.0  ;# 2fs/step
#rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2  
stepspercycle       10


# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens


# Periodic Boundary Conditions
cellBasisVector1     -75.1629982   0.0   0.0
cellBasisVector2     0.0    -78.31999779 0.0
cellBasisVector3     0.0    0.0  -98.59599972
cellOrigin          -12.303732872009277 19.206361770629883 -36.690704345703125

wrapAll             on


# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSizeX        80
PMEGridSizeY        80
PMEGridSizeZ        100
dcdUnitCell     yes
# mobile atom selection:
# protein
fixedAtoms              on
fixedAtomsFile          fixedatoms_backbone.pdb
fixedAtomsCol           B


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

# Minimization
minimize            10000
reinitvels          $temperature
$\endgroup$
  • $\begingroup$ The downvote(not by me) was given because Chemistry SE does not generally support software queries. However, a new materials (and molecular) modeling stack exchange just launched in a private beta to address questions like this. For example see materials.meta.stackexchange.com/questions/38/… $\endgroup$ – Cody Aldaz May 1 at 20:02
3
$\begingroup$

At the top of your config file, you imply that you want to perform an NVE calculation, but you’re actually doing NVT, because you have the Langevin thermostat turned on. Langevin works by giving the system a random “kick”, which is probably spiking the energy.

| improve this answer | |
$\endgroup$
  • $\begingroup$ Thank you for your answer. The configuration file was from one of the NAMD tutorials that they supplied on the website. I changed that file but I didn't remove commentations. That is why unrelated comments are in that file. $\endgroup$ – Onur Ozcan Jun 4 '18 at 23:06
  • $\begingroup$ @OnurOzcan That doesn’t change the fact that using a thermostat will occasionally cause the energy to jump due to the bath coupling. $\endgroup$ – pentavalentcarbon Jun 4 '18 at 23:36

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.