Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer

From: begüm alaybeyoğlu (
Date: Wed Dec 16 2015 - 03:46:10 CST

Hi Chitrak,

Thank you for the reply. I have checked everything you mentioned.

1. I merged the peptide-lipid-water system using psfgen. I will try the
TopoTools, but I think the problem is not really about the merging of the
peptide and water-lipid system. I tried minimizion and equilibration of the
water-lipid system (before adding the peptide and ions) as well and I get
the same error (and saw that H atoms overlap again).

2. I checked my PDBs and I don't have any atoms that were not assigned

3. As you mentioned, I have 13200 water molecules and when I saved the
coordinates of the equilibrated bilayer (at the end of the step7.1
production run) VMD messed up the number of the water molecules. So I had
to split the water molecules into 2 segments manually (1 segment for the
bilayer) and merged them using psfgen. I believe everythings OK now?

So, I am still not able to solve the problem.

Kind regards.


On Tue, Dec 15, 2015 at 8:46 PM, Chitrak Gupta <> wrote:

> Hi Begum,
> I have never used charmm27, but I have used charmm36 and have ran into
> this problem quite a few times. Here are my questions/suggestions:
> 1. How are you merging your lipid with your peptide? In my experience,
> TopoTools works a lot better than using psfgen
> 2. Make sure your merged PDB doesn't have anything funny. For example, if
> some atom has its X,Y,Z coordinates as 0.000,0.000,0.000, it basically
> means coordinates were not set for that atom. Look through your PDB (maybe
> generate a script to check it) whether you have such atoms.
> 3. Also look at the number of waters. When charmm-gui generates a psf/pdb,
> it assigns all the waters into one segment. Problem with psfgen is that it
> cannot handle more than 9999 waters within a segment. So, when you take a
> charmm-gui generated PDB and modify it using psfgen, your water numbers are
> completely messed up. You now have multiple waters with the same number.
> You will need to re-segment your waters, keeping 9999 waters in each
> segment.
> Hope this helps.
> Regards,
> Chitrak.
> On Tue, Dec 15, 2015 at 11:27 AM, begüm alaybeyoğlu <>
> wrote:
>> Dear NAMD users,
>> I am having trouble with the Charmm Gui generated POPE bilayer. After
>> having run all the minimization-equilibration-production steps, I ran a 25
>> ns production simulation (step.7.1) without any problems. What I wanted to
>> do was to get the last snapshot of my equilibrated bilayer, place my
>> peptide on top of it, autoionize the system and run a quick minimization &
>> equilibration before I start the peptide translocation simulation.
>> Now I keep getting the RATTLE error (for atoms of bilayer always) just
>> after the minimization is completed and I tried all of the previously
>> suggested solutions, such as decreasing the timestep or nonbondedFreq or
>> fullElectFrequency or stepspercycle and increasing the minimization steps
>> etc. When I plotted the energy I saw that around 2500 steps of minimization
>> was enough already. I tried slow heating of the system, but the error did
>> not change. By decreasing my dcdfreq to 10 steps, I observed that H atoms
>> (bound to C or N) actually start to overlap during the minimization, so the
>> cause of the error is probably this.
>> I have run many similar simulations with charmm27 before without any
>> problems.This is the first time I built the whole system from scratch
>> using the charmm36 parameters, so I am not sure what is going on. Any
>> suggestions are welcome.
>> Thanks.
>> Begum Alaybeyoglu

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