Re: Rattle Error During Equilibration of Lipid Bilayer Membrane

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Sun Feb 12 2006 - 21:11:29 CST

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
>>>>
>>>>
>>>>
>>>>
>>>>
>>

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