From: Life Sciences Inc (contact.lifesciences.inc_at_gmail.com)
Date: Mon Oct 26 2015 - 13:37:42 CDT
Yes they were equilibrated for a short time around 50ps ,, I think I
should equiliberate the system for a more time...
On Mon, Oct 26, 2015 at 7:01 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
> You had replied only to me, I am forwarding to the mailing list.
>
> What I meant is, maybe you can run it for a while with 1fs timestep, and
> then shift to 2fs before beginning your production run.
>
> Were your lipids already equilibrated at 303.15K?
>
>
> Best,
> Chitrak.
>
> On Mon, Oct 26, 2015 at 10:23 AM, Life Sciences Inc <
> contact.lifesciences.inc_at_gmail.com> wrote:
>
>> I tried to run it for 1fs it was fine with that, but as I need to do
>> production run so its better to use 2fs timestep and what do you mean by
>> Gentler heating ?? I have already simulated the pure lipid system without
>> flourophores with 303.15K temperature....
>>
>> On Mon, Oct 26, 2015 at 3:10 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
>> wrote:
>>
>>> In case you still see the problem, you could also try to reduce the
>>> timestep to 1fs for a while, and see if the error goes away. Another issue
>>> could be heating it too rapidly, since you have lipids in your system.
>>> Maybe try a gentler heating.
>>>
>>>
>>> Best,
>>> Chitrak.
>>>
>>> On Mon, Oct 26, 2015 at 2:59 AM, Tristan Croll <tristan.croll_at_qut.edu.au
>>> > wrote:
>>>
>>>> My guess here is that you need to include the line
>>>>
>>>>
>>>>
>>>> regenerate angles dihedrals
>>>>
>>>>
>>>>
>>>> at the end of your psfgen script (or choose this under the Options menu
>>>> in AutoPSF). One of the many changes between CHARMM27 and CHARMM36
>>>> forcefields is that angles and dihedrals are no longer explicitly defined
>>>> in patches, so without this line in your script any patch atoms will be
>>>> bouncing around unrestrained (which, in my experience, typically leads to
>>>> the below error in fairly short order).
>>>>
>>>>
>>>>
>>>> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
>>>> Behalf Of *Life Sciences Inc
>>>> *Sent:* Monday, 26 October 2015 10:43 AM
>>>> *To:* namd-l_at_ks.uiuc.edu
>>>> *Subject:* namd-l: constraint failure in Rattle algorithm for atom
>>>> 54134
>>>>
>>>>
>>>>
>>>> Dear All
>>>>
>>>>
>>>>
>>>> I am trying to run the simulation but I am getting this error of
>>>> constraint failure in Rattle algorithm for atom 54134!
>>>>
>>>>
>>>>
>>>> I am loading the psf with my trajectory and the structure seems goods,
>>>> also viewed the psf with last restart.coor file and everything seems fine.
>>>> I have also minimized the structure with 10,000 steps and then reran the
>>>> simulation but I got the same error on some other atom 40324. In my view
>>>> this is not the error of bad structure, if anyone has faced the similiar
>>>> problem and can get me out of this error, I will be really greatful.
>>>>
>>>>
>>>>
>>>> This is my Configuration File
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> structure noclash_final.psf
>>>>
>>>> coordinates noclash_final.pdb
>>>>
>>>>
>>>>
>>>> set temp 303.15
>>>>
>>>> outputName NPT_Prod_F3S # base name for output
>>>> from this run
>>>>
>>>> # NAMD writes two files at the
>>>> end, final coord and vel
>>>>
>>>> # in the format of
>>>> first-dyn.coor and first-dyn.vel
>>>>
>>>> set inputname NPT_Prod_F2
>>>>
>>>> bincoordinates $inputname.restart.coor # coordinates from last
>>>> run (binary)
>>>>
>>>> binvelocities $inputname.restart.vel # velocities from last
>>>> run (binary)
>>>>
>>>> extendedSystem $inputname.restart.xsc # cell dimensions
>>>> from last run (binary)
>>>>
>>>> restartfreq 50000 # 500 steps = every 1ps
>>>>
>>>> dcdfreq 2500
>>>>
>>>> dcdUnitCell yes # the file will contain unit cell
>>>> info in the style of
>>>>
>>>> # charmm dcd files. if yes, the
>>>> dcd files will contain
>>>>
>>>> # unit cell information in the
>>>> style of charmm DCD files.
>>>>
>>>> xstFreq 2500 # XSTFreq: control how often the
>>>> extended systen configuration
>>>>
>>>> # will be appended to the XST
>>>> file
>>>>
>>>> outputEnergies 2500 # 125 steps = every 0.25ps
>>>>
>>>> # The number of timesteps
>>>> between each energy output of NAMD
>>>>
>>>> outputTiming 2500 # The number of timesteps
>>>> between each timing output shows
>>>>
>>>> # time per step and time to
>>>> completion
>>>>
>>>>
>>>>
>>>> # Force-Field Parameters
>>>>
>>>> paraTypeCharmm on # We're using charmm type
>>>> parameter file(s)
>>>>
>>>> parameters fluorophore.prm
>>>>
>>>> parameters par_all36_cgenff.prm
>>>>
>>>> parameters par_all36_lipid.prm
>>>>
>>>> parameters par_all36_prot.prm
>>>>
>>>>
>>>>
>>>> # These are specified by CHARMM
>>>>
>>>> exclude scaled1-4 # non-bonded exclusion policy to
>>>> use "none,1-2,1-3,1-4,or scaled1-4"
>>>>
>>>> # 1-2: all atoms pairs that are
>>>> bonded are going to be ignored
>>>>
>>>> # 1-3: 3 consecutively bonded
>>>> are excluded
>>>>
>>>> # scaled1-4: include all the
>>>> 1-3, and modified 1-4 interactions
>>>>
>>>> # electrostatic scaled by
>>>> 1-4scaling factor 1.0
>>>>
>>>> # vdW special 1-4 parameters in
>>>> charmm parameter file.
>>>>
>>>> 1-4scaling 1.0
>>>>
>>>> switching on
>>>>
>>>> vdwForceSwitching yes; # New option for force-based
>>>> switching of vdW
>>>>
>>>> # if both switching and
>>>> vdwForceSwitching are on CHARMM force
>>>>
>>>> # switching is used for vdW
>>>> forces.
>>>>
>>>>
>>>>
>>>> # You have some freedom choosing the cutoff
>>>>
>>>> cutoff 12.0; # may use smaller, maybe 10.,
>>>> with PME
>>>>
>>>> switchdist 10.0; # cutoff - 2.
>>>>
>>>> # switchdist - where you start
>>>> to switch
>>>>
>>>> # cutoff - where you stop
>>>> accounting for nonbond interactions.
>>>>
>>>> # correspondence in charmm:
>>>>
>>>> # (cutnb,ctofnb,ctonnb =
>>>> pairlistdist,cutoff,switchdist)
>>>>
>>>> pairlistdist 14.0; # stores the all the pairs with
>>>> in the distance it should be larger
>>>>
>>>> # than cutoff( + 2.)
>>>>
>>>> stepspercycle 20; # 20 redo pairlists every ten
>>>> steps
>>>>
>>>> pairlistsPerCycle 2; # 2 is the default
>>>>
>>>> # cycle represents the number of
>>>> steps between atom reassignments
>>>>
>>>> # this means every 20/2=10 steps
>>>> the pairlist will be updated
>>>>
>>>>
>>>>
>>>> # Integrator Parameters
>>>>
>>>> timestep 2.0; # fs/step
>>>>
>>>> rigidBonds all; # Bound constraint all bonds
>>>> involving H are fixed in length
>>>>
>>>> nonbondedFreq 2; # nonbonded forces every step
>>>>
>>>> fullElectFrequency 4; # PME every step
>>>>
>>>>
>>>>
>>>> # Periodic Boundary conditions
>>>>
>>>> cellBasisVector1 118.431 0. 0. ;# vector to the next image
>>>>
>>>> cellBasisVector2 0. 118.431 0.
>>>>
>>>> cellBasisVector3 0. 0 90.6448
>>>>
>>>> cellOrigin 0.98007694 -0.51859881 -1.1731613 ;# the *center*
>>>> of the cell
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> wrapWater off; # wrap water to central cell
>>>>
>>>> wrapAll off; # wrap other molecules too
>>>>
>>>> wrapNearest off; # use for non-rectangular cells
>>>> (wrap to the nearest image)
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> # PME (for full-system periodic electrostatics)
>>>>
>>>> #source checkfft.str
>>>>
>>>>
>>>>
>>>> PME yes;
>>>>
>>>> PMEInterpOrder 6; # interpolation order (spline
>>>> order 6 in charmm)
>>>>
>>>> PMEGridSizeX 125; # should be close to the cell size
>>>>
>>>> PMEGridSizeY 125; # corresponds to the charmm input
>>>> fftx/y/z
>>>>
>>>> PMEGridSizeZ 100;
>>>>
>>>>
>>>>
>>>> #Constant Pressure Control (variable volume)
>>>>
>>>> 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 anisotropic system
>>>> like membrane
>>>>
>>>> useConstantRatio yes; # keeps the ratio of the unit
>>>> cell in the x-y plane constant A=B
>>>>
>>>>
>>>>
>>>> langevinPiston on; # Nose-Hoover Langevin piston
>>>> pressure control
>>>>
>>>> langevinPistonTarget 1.01325; # target pressure in bar 1atm =
>>>> 1.01325bar
>>>>
>>>> langevinPistonPeriod 2000.0; # oscillation period in fs.
>>>> correspond to pgamma T=50fs=0.05ps
>>>>
>>>> # f=1/T=20.0(pgamma)
>>>>
>>>> langevinPistonDecay 1000.0; # oscillation decay time.
>>>> smaller value correspons to larger random
>>>>
>>>> # forces and increased coupling
>>>> to the Langevin temp bath.
>>>>
>>>> # Equall or smaller than piston
>>>> period
>>>>
>>>> langevinPistonTemp $temp; # coupled to heat bath
>>>>
>>>>
>>>>
>>>> # Constant Temperature Control
>>>>
>>>> langevin on; # langevin dynamics
>>>>
>>>> langevinDamping 1.0; # damping coefficient of 1/ps
>>>> (keep low)
>>>>
>>>> langevinTemp $temp; # random noise at this level
>>>>
>>>> langevinHydrogen off; # don't couple bath to hydrogens
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> # run
>>>>
>>>> run 50000000;
>>>>
>>>
>>>
>>
>
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