From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Oct 26 2015 - 13:01:16 CDT
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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