From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Sun Feb 12 2006 - 15:40:20 CST
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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