From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Feb 04 2007 - 08:15:38 CST
Ok, sorry for my misunderstanding. Given that I'd also suggest two
additional things:
-set your pairlistdist to be at least 2-3A larger than your cutoff (to
avoid atoms drifting into nonbond range)
-Expand your pme grid to be at least 1 point per angstrom
You'll then just need to look at the trajectories, preferably with the
proper wrapping on. I'll be interested to hear what's going on, because
I've never seen a problem like this with the pope bilayer patch.
Peter
Himanshu Khandelia wrote:
> I am using the the vmd POPE bilayer patches. Will try to look at the dcd
> with a write frequeny of 1 and update,
>
> Thank you,
>
> -himanshu
>
>
>
> On Sat, 3 Feb 2007, Peter Freddolino wrote:
>
>
>> 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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