Re: AW: Energy minimization of membrane

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Fri Feb 03 2012 - 05:20:29 CST

On Fri, Feb 3, 2012 at 4:49 PM, kanchi subbarao rao <ksubbu85_at_gmail.com>wrote:

> hi Maroun
>
> Let me know how you are running minimization with out mention PBC in your
> simulation in NAMD
>
> The box size (whatever you mention in PBC it should be cover the whole
> system). It is require to calculate PME (electrostatic) calculations.you
> can use small grid size to calculate accurate,
> by using keyword
> PME yes
> PMEGridSpacing 1.0
>
> regards
> subbarao kanchi
> physics Dept
> IISC bangalore
>
>
>
> On Fri, Feb 3, 2012 at 4:28 PM, R. Charbel Maroun <
> charbel.maroun_at_inserm.fr> wrote:
>
>> Hi,
>>
>> Thanks for the feedback. It's not that I didn't want to use PBC. I
>> just wanted to know if it was necessary for a minimization. By the
>> way, before running MD, the system must be well minimized, otherwise
>> it might become unstable during the trajectory. It's part of the
>> equilibration step, before production.
>>
>> I used CHARMM-GUI for building my membrane system. I ran last night an
>> energy minimization with PME and PBC for just the
>> water molecules and the K and Cl ions; lipids and receptor fixed (when
>> you use PME you need PBC). The question is what values to use for
>> PMEGridSize and cellBasisVector? What I did is that for the first set
>> I measured approximately on the screen the dimensions of the box size;
>> for the second set I just guessed slightly larger values. I don't know
>> if that's right.
>>
>> The results of the minimization show that the ordered structure of
>> waters away from the phospholipid head groups was lost (good!). The
>> water layers above and below got flattened, more compact along the
>> axis perpendicular to the membrane, and wider in the axes of the
>> membrane. When I ran a minimization without PBC, one water molecule
>> would always escape from the box and get wild coordinates. NAMD would
>> then stop if you tried to use this coordinate set for further
>> calculations.
>>
>> # PBC
>> cellBasisVector1 90.0 0.0 0.0
>> cellBasisVector2 0.0 109.0 0.0
>> cellBasisVector3 0.0 0.0 90.0
>> cellOrigin 0.0 0.0 2.0
>> wrapAll on
>> wrapWater on
>> dcdUnitCell yes
>>
>> # PME
>> PME yes
>> PMEGridSizeX 85
>> PMEGridSizeY 85
>> PMEGridSizeZ 103
>>
>>
>> Any suggestions ?
>>
>> Cheers,
>>
>> C Maroun
>>
>> Norman Geist <norman.geist_at_uni-greifswald.**de<norman.geist_at_uni-greifswald.de>>
>> a écrit :
>>
>>
>> Hi,
>>>
>>>
>>>
>>> I'm not a specialist in bio chemistry, more on IT, but I would expect
>>> your
>>> membrane as not big enough to be realistic without its periodic copys.
>>> So it
>>> won't behave good, as it would be in vacuum, and the best energy
>>> conformation achieved then, wouldn't be the one you want. I would expect
>>> that it will relax more into a strange conformation, as in a realistic
>>> one.
>>> Also, if you don't set PBC, your solvent will diffuse away, if there is
>>> one.
>>>
>>>
>>>
>>> What's the reason for not want to set PBC in minimization? If you want to
>>> look if your system want to expand, you can try that out with some
>>> different
>>> box sizes, and with dynamics, not minimization as minimization will not
>>> move
>>> the system much.
>>>
>>>
>>>
>>> Correct me if required ;)
>>>
>>>
>>>
>>> Best wishes
>>>
>>>
>>>
>>> Norman Geist.
>>>
>>>
>>>
>>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.**edu<owner-namd-l_at_ks.uiuc.edu>]
>>> Im Auftrag
>>> von Boyang Wang
>>> Gesendet: Freitag, 3. Februar 2012 06:31
>>> An: R. Charbel Maroun
>>> Cc: namd-l_at_ks.uiuc.edu
>>> Betreff: Re: namd-l: Energy minimization of membrane
>>>
>>>
>>>
>>> Hi Charbel,
>>>
>>>
>>>
>>> I think PBC is necessary, but keep in mind that calculations will be much
>>> slower.
>>>
>>>
>>>
>>> Best,
>>>
>>> Boyang
>>>
>>>
>>>
>>> On Thu, Feb 2, 2012 at 8:37 PM, R. Charbel Maroun <
>>> charbel.maroun_at_inserm.fr>
>>> wrote:
>>>
>>> Hello,
>>>
>>> When we do energy minimization with NAMD of a protein-membrane system,
>>> do we have to give PBC in the script, just like for a
>>> molecular dynamics calculation or is this implicitely taken into
>>> consideration? If not, that means that the protein-membrane system is
>>> in vacuum and could become unstable during minimization.
>>>
>>> Greetings,
>>>
>>> C Maroun
>>>
>>>
>>>
>>>
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>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Boyang Wang, Ph.D.
>>>
>>>
>>>
>>
>>
>>
>>
>>
>>
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>>
>>
>>
>>
>

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