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

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Feb 03 2007 - 08:38:58 CST

I should clarify a bit more -- you're not using one of the POPC or POPE
bilayers that are built in to VMD right? I remember you were recently
adding in a different lipid with the membrane plugin. Are you currently
using your new bilayer or one of the ones that comes with VMD? In any
case, you should rerun the dynamics portion with a dcd frequency of 1,
and have a look at the atoms that namd reports as moving too fast to see
what the problem is (remember that NAMD atoms are 1-indexed, whereas VMD
atoms are 0-indexed).
Peter

Himanshu Khandelia wrote:
> 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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