Re:

From: jeevan gc (gcjeevanbdr_at_gmail.com)
Date: Sun Feb 10 2019 - 09:52:26 CST

Thank you for your valuable suggestions. As you suggested, I will impose
distanceXY coordinate harmonic restraint on my system.

Jeevan

On Mon, Jan 28, 2019 at 6:04 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi,
>
> You can restrain the center of mass of the protein laterally using a
> hamonic restraint on a distanceXY coordinate, between a subset of atoms of
> the protein (alpha carbons?) and a dummy atom.
> http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html
>
> Best,
> Jerome
>
> On Sat, 26 Jan 2019 at 16:49, jeevan gc <gcjeevanbdr_at_gmail.com> wrote:
>
>> Hi Josh,
>>
>> Thank you for your valuable suggestions.
>>
>> I completely agree with you that the protein should be allowed to move
>> in the membrane system. As you suggested, I decided to use
>> selectConstraints to only use lateral constraints. However, for the
>> multimeric proteins like dimer, tetramer, pentamer etc., the drift caused
>> some problems, especially if I want to count hydration of pore (for example
>> in calcium channels tetrameric proteins) along the membrane z-axis.
>>
>> These problems could be solved by pbcwrap after simulations as well.
>>
>> Do you recommend using a higher damping coefficient (increase to 2 or 3
>> ps-1) instead of constraints?
>>
>> Thank you.
>>
>> Jeevan
>>
>>
>>
>> On Fri, Jan 25, 2019 at 9:59 AM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
>> wrote:
>>
>>> If you want to disallow lateral protein motion completely, why not just
>>> use constraints?
>>> http://www.ks.uiuc.edu/Research/namd/2.13/ug/node27.html#SECTION00086200000000000000 Just
>>> tag the protein and use selectConstraints to only use lateral constraints.
>>> However, in practice you really shouldn't care if your membrane drifts, and
>>> my usual practice has been to ignore it unless I need to make an animation.
>>> Proteins and membranes move, and that's just a fact of life. I'd
>>> recommend turning off wrapAll, and then just rewrapping afterward in VMD,
>>> possibly even recentering the protein prior to rewrapping.
>>>
>>> -Josh
>>>
>>>
>>>
>>>
>>> On 2019-01-24 16:00:34-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
>>>
>>> Dear all,
>>> We have come across an issue on protein and membrane regular MD
>>> simulations. We are also aware of the fact that this issue is just about
>>> visualization and should be taken care by the Periodic Boundary
>>> Conditions. The membrane size is sufficient enough to avoid any overlap in
>>> periodic image as the protein drift from the edge of the membrane. The wrap
>>> all is also turned on. The namd mailing list provided us important
>>> information and suggestions about this issue but still not able to
>>> completely solve this issue.
>>> Below are list of simulations we would like to practice to avoid the
>>> drift of the protein from the membrane edge.
>>> 1. Increased the step6.6 equlibration simulation step obtained from
>>> CHARMM-GUI to 10ns or higher.
>>> 2. Increase the damping constant from 1 to 2 ps.
>>> 3. Increased the size of the membrane.
>>> 4. Applied the minimal restraint to the protein and the membrane system--0000000000006a6e8c05818c2ee7--

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