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Mycom 200 Vmd Manual Software
From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Fri Aug 12 2016 - 15:21:21 CDT
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Hi Josh,
GAS COMPRESSOR DIVISION OVERHAUL MANUAL MYCOM VR Series Screw Compressor Overhaul Manual Supersedes all previous version. This information is for reference use only and subject to change without notice Revision 3 (September 01,2000) Page 1 of 51. Under the MYCOM brand name, Mayekawa's compressors are in use in industrial refrigeration/freezing, heat pump, and gas markets around the world. Leveraging the thermal technology we have fostered through years of experience, we have developed compressors of the highest quality and consistency.
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:
Torrent ray lamontagne. #############################################################
## JOB DESCRIPTION ##
#############################################################
# Constant Force Pulling for fully equilibrated alphaVbeta3
# 0.5 nanoseconds with a force of 10 (about 700 pN)
http://xsybag.xtgem.com/Blog/__xtblog_entry/19217844-mac-browser-name#xt_blog. #############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure alphaVbeta3_wb.psf
coordinates alphaV_full_equil.pdb
outputName first_fully_equilibrated_alphaV

set temperature 310
Data rescue professional 4 3 full crack for mac. # 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
}
Mycom 200 Vmd Manual Download# 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?
}
Mycom 200 Vmd Manual Software

set temperature 310
Data rescue professional 4 3 full crack for mac. # 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
}
Mycom 200 Vmd Manual Download# 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?
}
Mycom 200 Vmd Manual Software#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc.)
Sw tanaka t22 hd jurassic terbaru 2018. constantforce yes
consforcefile first_sim_attempt.ref
Authentec fingerprint software for mac. #############################################################
## EXECUTION SCRIPT ##
#############################################################
#Minimization
if {0} {
minimize 10000
reinitvels $temperature
}
 American roulette table layout.
run 250 ;# 0.5ns
On Fri, Aug 12, 2016 at 2:45 PM, Vermaas, Joshua 
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
>
>
Next message:Nuno Sousa Cerqueira: 'Re: using vslab in vmd'
Previous message:Vermaas, Joshua: 'Re: Minimization--Number of Timesteps'
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Brand:MYCOMType:NH3/CO2 PlantStock number:M15-6040Cooling capacity:540 kWRefrigerant: R717 (NH3/Ammonia), R744 (CO2)Refrigerant Content:400/1500 kgVoltage:400 VoltsDimensions:N.A./N.V.T. mmYear:2004Number in stock:1 piece(s)Price:Description:A young, well maintained Mycom NH3/CO2 compressor plant with 540kW at -41,5°C. The plant exist out of three Mycom N160VLD screw compressors (NH3), three Mycom C6HK piston compressors (CO2), Baltimore evaporating condenser VXC 265, low-stage and intermediate pressure vessels, etc. The six compressors are all frequency driven (Danfoss) and all are controlled by Siemens S7 PLC. All the certificates and manuals of this installation are present. More detailed information see attached PDF.