Re: "atoms moving too fast" error in bilayer simulation

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Sat Feb 03 2007 - 01:21:35 CST

The membrane was made from the vmd membrane plugin. When I said bad
contacts, I meant that the initial energy of the system was diverging
(99999999.9999)

Towards the end of minimization, the gradient tolerance is 0.015, but the
VDW energy term is still infinite (99999999.9999). I guess I need more
minimization ?

-Himanshu

On Fri, 2 Feb 2007, Peter Freddolino wrote:

> Hi Himanshu,
> is this using a home-built lipid bilayer? The bilayers that come with
> VMD's membrane plugin should not have any bad contacts...
>
> What is the last gradient tolerance reported by NAMD during the
> minimization process? If it's much larger than, say, 1, you may just not
> be minimizing the system for long enough to get rid of all the clashes,
> so the system explodes as soon as you allow it to move freely. Have you
> looked to see if the bad contacts appear to be eliminated at the end of
> minimization?
>
> Peter
>
> Himanshu Khandelia wrote:
> > Hi,
> >
> > I am using VMD's membrane plugin to construct a membrane, solvating it,
> > and then trying to equilibrate it. The membrane generated by VMD does have
> > a lot of bad contacts, but I thought NAMD would handle them.
> >
> > I keep getting the "atoms moving too fast" error as soon as I start
> > heating the bilayer after minimzation. I have tried the following, but
> > nothing works so far:
> >
> > - heating in very small increments (~ 3 degrees every 3000 steps)
> > - larger cutoffs (16 A)
> > - with/without constraints on head groups
> > - larger box sizes (than suggested by the minmax of water)
> >
> > Any suggestions into what might be going wrong ? The config file is
> > attached with this email,
> >
> > Thank you !
> >
> > -Himanshu
> > ------------------------------------------------------------------------
> >
> > set MOL pope-water
> >
> > set temp 500
> >
> > set xbox 70
> > set ybox 70
> > set zbox 94
> >
> > structure ${MOL}.psf
> > coordinates ${MOL}.pdb
> > temperature 0
> > parameters par_all27_prot_lipid.prm
> > paraTypeCharmm on
> >
> > outputEnergies 100
> > outputTiming 100
> > xstFreq 100
> > dcdFreq 500
> > wrapAll on
> >
> > timestep 1
> > nonBondedFreq 2
> > fullElectFrequency 4
> > stepsPerCycle 20
> >
> > exclude scaled1-4
> > 1-4scaling 1.0
> > switching on
> > switchDist 14
> > cutoff 16
> > pairlistdist 16
> >
> > cellBasisVector1 $xbox 00.00 00.00
> > cellBasisVector2 00.00 $ybox 00.00
> > cellBasisVector3 00.00 00.00 $zbox
> > cellOrigin -0.58 -0.78 0.056
> >
> > Pme on
> > PmeGridsizeX 60
> > PmeGridsizeY 60
> > PmeGridsizeZ 96
> >
> > #########################################
> > # CONSTRAINTS
> > #########################################
> > constraints on
> > consRef ${MOL}-cons.pdb
> > consKFile ${MOL}-cons.pdb
> > consKCol B
> >
> > #########################################
> > # PRESSURE AND TEMPERATURE CONTRON
> > #########################################
> >
> > langevin on
> > langevinDamping 5
> > langevinTemp $temp
> > langevinHydrogen no
> >
> > useflexiblecell yes
> > langevinPiston on
> > langevinPistonTarget 1.01325
> > langevinPistonPeriod 100
> > langevinPistonDecay 50
> > langevinPistonTemp $temp
> >
> > binaryoutput off
> > outputname ${MOL}-equil
> >
> > # GET INIT. ENERGY
> > minimize 0
> >
> > ###########
> > # MINIMIZE
> > ###########
> >
> > minimize 10000
> > output ${mol}-cons
> >
> > #######
> > # HEAT
> > #######
> >
> > set tem 1
> > while { $tem <= 500 } {
> > langevinTemp $tem
> > run 3000
> > set tem [expr $tem + 3]
> > }
> >
>

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