**From:** Arneh Babakhani (*ababakha_at_mccammon.ucsd.edu*)

**Date:** Sun Feb 12 2006 - 21:11:29 CST

**Next message:**Chandra Ramananjara: "Re: vmd-l: Problem with VMD 'animate' command"**Previous message:**Morad Alawneh: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**In reply to:**Morad Alawneh: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**Next in thread:**Dan Strahs: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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:**Chandra Ramananjara: "Re: vmd-l: Problem with VMD 'animate' command"**Previous message:**Morad Alawneh: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**In reply to:**Morad Alawneh: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**Next in thread:**Dan Strahs: "Re: Rattle Error During Equilibration of Lipid Bilayer Membrane"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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