From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Sun Feb 04 2007 - 06:11:03 CST
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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