Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Dec 16 2015 - 11:23:39 CST

Hi Begum,

Oops, sorry about that. This is the link I meant

https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks

Thanks for letting me know about the auto none part. Didn't know this was a
possibility as well, good to learn.

Best regards,
Chitrak.

On Wed, Dec 16, 2015 at 11:21 AM, begüm alaybeyoğlu <bgmalay_at_gmail.com>
wrote:

> 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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