Re:

From: jeevan gc (gcjeevanbdr_at_gmail.com)
Date: Sat Jan 26 2019 - 09:45:22 CST

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.
> 5. NPT/NVT minimization
> We tried Simulation #1, it didn't help. The protein drifted from the edge
> of the membrane. Is it necessary to increase damping coefficient to 2ps
> as suggested by James Starlight?
> If these only visualization issues, increasing the size of the membrane
> will increase the simulation time and we don't benefit much.
> Simulation #4, restraining either protein of membrane COM may create an
> artifact in protein membrane interactions.
> As CHARMM-GUI minimization steps suggested, we performed step6.1 and
> step6.2 in NVT, step6.3 to step6.6 in NPT ensemble. Production run was
> performed on NPT.
> Are there any best practices to avoid such drift of protein in the
> membrane? Any advice will be greatly appreciated.
>
> Thank you in advance.
> Jeevan
> --
> *Jeevan B. GC, Ph.D*
> *Post Doctoral Research Associate*
> *Department of Pharmaceutical Sciences*
> *Washington State University*
> *Spokane, WA 99224 , **USA*
>
>

-- 
*Jeevan B. GC, Ph.D*
*Post Doctoral Research Associate*
*Department of Pharmaceutical Sciences*
*Washington State University*
*Spokane, WA 99224 , **USA*

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