VMD-L Mailing List

From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Sat Aug 13 2016 - 16:36:27 CDT

Yeah, it definitely was moving at a very high velocity. It was V-shaped
originally. That is why I was wondering if it was equilibrated and
minimized correctly. Could this be a result of the system not reaching its
lowest energy state? This was after only 4 picoseconds with a force of 1
kcal/mol-angstrom^2. Let me know what you think.

Thanks!

Jack

On Sat, Aug 13, 2016 at 3:37 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Jack,
>
> That is one wickedly extended protein. Was it always like that? It looks
> like the piece in the lower right blew out of the waterbox at quite a high
> velocity, so it isn't surprising to me that this simulation crashed.
>
> -Josh
>
> On 08/13/2016 08:51 AM, Jackson Cavett wrote:
> I gave it a try and ran into the same problem. I didn't do any constraint
> scaling, and the following are the harmonic restraint parameters I used:
>
> constantforce yes
> consforcefile alphaV_equil_harm_restraint.ref
>
> constraints on
> consref alphaV_equil.pdb
> conskfile alphaV_equil_harm_restraint.ref
> conskcol B
> constraintScaling 1.0
>
>
> Please let me know if I have anything setup wrong or if there is a change
> that might help. I have attached a screenshot of what the output looks like
> after about 4 picoseconds. For this simulation I used a force of 1
> kcal/mol-angstrom^2, which I don't think is huge. Hopefully that picture
> can help make sense of what is going wrong.
>
> Thanks Again,
>
> Jack
>
>
>
>
>
> On Fri, Aug 12, 2016 at 3:56 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<
> mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
> Ok. Have you tried using constraints rather than fixing the atom
> positions? (http://www.ks.uiuc.edu/Research/namd/2.11/ug/node27.html#
> SECTION00086200000000000000) In my limited experience with SMD, fixing
> atoms causes problems when particles get close to the fixed atoms, and you
> get failures of those specific atoms that venture near the brick wall. Your
> minimization is probably sufficient. As a general rule, 1000 steps is
> normally enough to start a unequilibrated simulation, and 2000 might be
> needed for tough cases. Anything more than that generally doesn't help me,
> and instead instabilities are the result of me doing something dumb (like
> piercing a ring or putting two atoms exactly on top of one another). But,
> since this came from an existing trajectory, its probably a fixed atom
> problem.
>
> -Josh
>
> On 08/12/2016 02:21 PM, Jackson Cavett wrote:
> 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<
> mailto:Joshua.Vermaas_at_nrel.gov><mailto:Joshua.Vermaas_at_nrel.gov<mailto:
> 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
>
>
>
>
>
>