Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer

From: begüm alaybeyoğlu (bgmalay_at_gmail.com)
Date: Wed Dec 16 2015 - 10:21:17 CST

Dear Chitrak,

Thanks a lot for your suggestions (btw, i believe you copied the wrong link
for TopoTools).

Turns out, the "auto none" command i placed in the segment MEMB { } block
(segment for the bilayer) during the psf generation for the lipid-water
system (because the number of water molecules was higher than 9999) caused
the error. The angles and dihedrals for the lipid atoms was missing in the
generated psf. I removed that and now I have the angles and dihedrals set
correctly for my bilayer. Now, everything is working just fine.

Kind regards,

Begum

On Wed, Dec 16, 2015 at 5:21 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> Hi Begum,
>
> Did you remove the overlapping atoms after merging the two structures?
> This is how TopoTools does it
>
>
> https://www.google.com/maps/@39.657705,-79.9833983,3a,75y,336.15h,68.14t/data=!3m6!1e1!3m4!1sDtWl3tqzmk70PFFMQ0EqRQ!2e0!7i13312!8i6656
>
>
> If you follow the instructions given here and also renumber your waters,
> it should be working.
>
>
> The other potential issue is the periodic box dimensions. How are you
> setting them? I would strongly recommend using the same PBC that the *.inp
> scripts generated by charmm-gui has.
>
>
> This should hopefully solve the issue.
>
>
> Best regards,
> Chitrak.
>
> On Wed, Dec 16, 2015 at 4:46 AM, begüm alaybeyoğlu <bgmalay_at_gmail.com>
> wrote:
>
>> 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
>> coordinates.
>>
>> 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.
>>
>> Begum
>>
>>
>> On Tue, Dec 15, 2015 at 8:46 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
>> 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 <bgmalay_at_gmail.com>
>>> 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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