**From:** Dan Strahs (*dstrahs_at_pace.edu*)

**Date:** Mon Feb 13 2006 - 11:30:35 CST

**Next message:**John Stone: "Re: vmd-l: Problem with VMD 'animate' command"**Previous message:**snoze pa: "computer network"**Maybe in reply to:**Morad Alawneh: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**Next in thread:**Arneh Babakhani: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi:

Two things: I understand that DMPC has approximately the same density

as water; thus, 11,500 waters (or 34,500) requires a cube with a ~70.1

side or 3.44x10^5 A^3. Your system has nearly 38,900 atoms (based on the

200 DMPC/5100 waters); thus, I would expect you need ~3.88x10^5 A^3 or a

cube of side ~72.9. I think your cell may be too small, and NAMD can't

equilibrate the size to escape the inevitable RATTLE error. But this is

all based on comparing your cell to a water cell - I have no experience

with DMPC.

If this isn't helping, I would suggest dumping coordinates at a high

frequency and using VMD to watch the system, particularly the water that

gives the RATTLE error. In the past, I successfully tracked errors in

CHARMM that caused SHAKE errors using this protocol.

Dan Strahs

On Sun, 12 Feb 2006, Arneh Babakhani wrote:

*> Hi Morad,
*

*>
*

*> Yep, all of the below is correct. Still no good, still aborting. I
*

*> even went back and did an additional 10,000 steps of minimization. Then
*

*> when I tried to heat it up again, it gradually heated up to 330K, stayed
*

*> constant at the temperature for a while (indicating that heating was
*

*> complete), then aborted again.
*

*>
*

*> Thanks again,
*

*>
*

*> Arneh
*

*>
*

*> Morad Alawneh wrote:
*

*>
*

*> > *Hi Arneh,
*

*> >
*

*> > In this case try do what I did which helped me to get rid of this error:
*

*> >
*

*> > 1) make sure your box is big enough; e.g. let x length be larger by 2A
*

*> > from your atoms for each side, and do it for the other axises
*

*> >
*

*> > 2) make sure these parameters are the same in all your configuration
*

*> > files: switching, switchDist, and cutoff
*

*> >
*

*> > 3) check the following
*

*> > timestep = 2.0
*

*> > fullElectFrequency = 2
*

*> > nonbondedFreq = 1
*

*> >
*

*> > Note: **fullElectFrequency * **nonbondedFreq <= 4.0
*

*> >
*

*> > That is my way, I hope it will work for you
*

*> > *
*

*> >
*

*> > *
*

*> > *
*

*> >
*

*> >
*

*> > /*Morad Alawneh*/
*

*> >
*

*> > *Department of Chemistry and Biochemistry*
*

*> >
*

*> > *C100 BNSN, BYU*
*

*> >
*

*> > *Provo, UT 84602*
*

*> >
*

*> >
*

*> >
*

*> > Arneh Babakhani wrote:
*

*> >
*

*> >> Hi Morad, thank you for your suggestion.
*

*> >>
*

*> >> I didn't explicitly specify the basis vectors; I used the previous
*

*> >> dimensions, from the xsc file. Those dimensions are about
*

*> >> ~71x71x71. I took your suggestion of increasing the PME gridsize to
*

*> >> be >=1.5 times that length(~110x110x110). Indeed, that did help; the
*

*> >> simulation ran for much longer than it did before, but it still
*

*> >> aborted prematurely, with the same error. So although that might have
*

*> >> been part of the problem, it appears there's still something else
*

*> >> going on here.
*

*> >>
*

*> >> In any case, thank you for your help. Would greatly appreciate any
*

*> >> further ideas.
*

*> >>
*

*> >> Regards,
*

*> >>
*

*> >> Arneh
*

*> >>
*

*> >>
*

*> >>
*

*> >> Morad Alawneh wrote:
*

*> >>
*

*> >>> *Hi,
*

*> >>>
*

*> >>> It seems to me that you don't have periodic boundary for your
*

*> >>> system, and once you build that you have to make PMEGridSize to be
*

*> >>> >= 1.5 of the length of that axis.
*

*> >>>
*

*> >>> I hope that will fix your problem.
*

*> >>> *
*

*> >>>
*

*> >>>
*

*> >>>
*

*> >>> /*Morad Alawneh*/
*

*> >>>
*

*> >>> *Department of Chemistry and Biochemistry*
*

*> >>>
*

*> >>> *C100 BNSN, BYU*
*

*> >>>
*

*> >>> *Provo, UT 84602*
*

*> >>>
*

*> >>>
*

*> >>>
*

*> >>> Arneh Babakhani wrote:
*

*> >>>
*

*> >>>> Dear NAMD community,
*

*> >>>>
*

*> >>>> I constructed and solvated a lipid bilayer membrane. This consists
*

*> >>>> of 200 DMPC lipids (100 per monolayer), about 5100 water
*

*> >>>> molecules, for a total of ~40,000 atoms.
*

*> >>>>
*

*> >>>> I conducted 10,000 steps of minimization, ultimately achieving a
*

*> >>>> gradient tolerance of ~2.91. At the end of this minimization, I
*

*> >>>> zeroed the velocities of all atoms. No problem here . . .
*

*> >>>>
*

*> >>>> I then gradually heated up my system, over 2500 steps (2fs
*

*> >>>> timestep), to 330K. Looking at the plot of the temperature, the
*

*> >>>> system does heat up gradually, eventually plateauing out at 330K,
*

*> >>>> towards the end of the run. No problem here . . .
*

*> >>>>
*

*> >>>> I then turn on constant pressure and attempt to run for another
*

*> >>>> 2500 steps. The temperature spikes from 330K to ~375K, by the
*

*> >>>> second step! (I am implementing langevin temp control). The temp.
*

*> >>>> gradually decreases through the course of the simulation, but it
*

*> >>>> never quite gets back down to 330K. NAMD prematurely aborts
*

*> >>>> halfway through the run, at about 350K, giving the following error:
*

*> >>>>
*

*> >>>> ERROR: Constraint failure in RATTLE algorithm for atom 13561!
*

*> >>>>
*

*> >>>> ERROR: Constraint failure; simulation has become unstable.
*

*> >>>>
*

*> >>>> ERROR: Exiting prematurely.
*

*> >>>>
*

*> >>>>
*

*> >>>> I found through some trial & error that by increasing the langevin
*

*> >>>> Damping parameter, I can decrease the magnitude of this initial
*

*> >>>> temperature spike (although I can't get rid of it completely, very
*

*> >>>> strange). By decreasing this spike, the system comes back down to
*

*> >>>> 330K much faster, and the simulation proceeds to completion (with
*

*> >>>> langevin Damping = 7).
*

*> >>>>
*

*> >>>> I then try to run a 1 ns equilibration of my membrane, again using
*

*> >>>> lang. Damping = 7 (since this seemed to work for the constant
*

*> >>>> pressure run). This runs for about 850 ps and then aborts, with
*

*> >>>> the same RATTLE algorithm error. However, during this
*

*> >>>> equilibration, the temp. stays constant, as does the pressure (no
*

*> >>>> spikes), and nothing else is observably wrong. I repeated the
*

*> >>>> attempt for lang. Damping =5, and 9, no joy, still aborts.
*

*> >>>>
*

*> >>>> Would greatly appreciate any ideas? (I've pasted my conf file
*

*> >>>> below for reference)
*

*> >>>>
*

*> >>>> Regards,
*

*> >>>>
*

*> >>>> Arneh
*

*> >>>>
*

*> >>>> #############################################################
*

*> >>>> # 1NS equilibration dmpc lipid bilayer in a Water Box
*

*> >>>> #############################################################
*

*> >>>> structure ../common/solvated.psf
*

*> >>>> coordinates ../common/solvated.pdb
*

*> >>>> bincoordinates lipwaterconstpress2.coor
*

*> >>>> binvelocities lipwaterconstpress2.vel
*

*> >>>> extendedsystem lipwaterconstpress2.xsc
*

*> >>>>
*

*> >>>> set temperature 330
*

*> >>>> set outputname lipwaterequil1
*

*> >>>>
*

*> >>>> firsttimestep 0
*

*> >>>>
*

*> >>>> ## SIMULATION PARAMETERS ##
*

*> >>>>
*

*> >>>> paraTypeCharmm on
*

*> >>>> parameters ../common/par_all27_prot_lipid.inp
*

*> >>>>
*

*> >>>> # Force-Field Parameters
*

*> >>>> exclude scaled1-4
*

*> >>>> 1-4scaling 1.0
*

*> >>>> cutoff 10.
*

*> >>>> switching on
*

*> >>>> switchdist 9.
*

*> >>>> pairlistdist 11.5
*

*> >>>>
*

*> >>>>
*

*> >>>> # Integrator Parameters
*

*> >>>> timestep 2.0 ;# 2fs/step
*

*> >>>> rigidBonds all ;# needed for 2fs steps
*

*> >>>> nonbondedFreq 1
*

*> >>>> fullElectFrequency 2
*

*> >>>> stepspercycle 10
*

*> >>>>
*

*> >>>>
*

*> >>>> # Constant Temperature Control
*

*> >>>> langevin on ;# do langevin dynamics
*

*> >>>> langevinDamping 7 ;# damping coefficient (gamma) of 9/ps
*

*> >>>> langevinTemp $temperature
*

*> >>>> langevinHydrogen off ;# don't couple langevin bath to hydrogens
*

*> >>>>
*

*> >>>> wrapAll on
*

*> >>>>
*

*> >>>> # PME (for full-system periodic electrostatics)
*

*> >>>> PME yes
*

*> >>>> PMEGridSizeX 64
*

*> >>>> PMEGridSizeY 64
*

*> >>>> PMEGridSizeZ 64
*

*> >>>>
*

*> >>>> # Constant Pressure Control (variable volume)
*

*> >>>> useGroupPressure yes ;# needed for rigidBonds
*

*> >>>> useFlexibleCell no
*

*> >>>> useConstantArea no
*

*> >>>>
*

*> >>>> langevinPiston on
*

*> >>>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
*

*> >>>> langevinPistonPeriod 100.
*

*> >>>> langevinPistonDecay 200.
*

*> >>>> langevinPistonTemp $temperature
*

*> >>>>
*

*> >>>> # Output
*

*> >>>> outputName $outputname
*

*> >>>> restartfreq 500 ;# 500steps = every 1ps
*

*> >>>> dcdfreq 500
*

*> >>>> outputEnergies 100
*

*> >>>> outputPressure 100
*

*> >>>>
*

*> >>>> run 500000 ; # 1ns
*

*> >>>>
*

*> >>>>
*

*> >>>>
*

*> >>>>
*

*> >>>>
*

*> >>
*

*>
*

*>
*

**Next message:**John Stone: "Re: vmd-l: Problem with VMD 'animate' command"**Previous message:**snoze pa: "computer network"**Maybe in reply to:**Morad Alawneh: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**Next in thread:**Arneh Babakhani: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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