AW: Reg: movement of protein outside box

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jun 10 2014 - 07:26:58 CDT

As long as there’s no constant linear momentum, I guess there’s no problem, simply Brownian motion. Otherwise it may be effects like “center of mass drift” due long range electrostatics (PME) which represents a high center of mass motion. This can be controlled by the namd options “zeromomentum” and “commotion”.

 

Norman Geist.

 

Von: Akshay Bhatnagar [mailto:akshaybhatnagar2790_at_gmail.com]
Gesendet: Dienstag, 10. Juni 2014 14:19
An: Norman Geist
Betreff: Re: namd-l: Reg: movement of protein outside box

 

Thank you very much for your suggestions and kind help

But, in my system, the amino acid i am simulating is there at the center position already which i checked through the command "measure center $protein" and so is the water box. so, should i use the “pbc wrap –all –compound res –center com –centersel protein”? , Also I wanted to ask that is this diffusion a normal process after equilibration or is it due to bad system or bad parameters in the configuration file. Actually what could be the reason for diffusion if the system is already at the origin position.

 

Thanking you

With Regards

Akshay Bhatnagar

PhD Student

BITS Pilani Hyderabad Campus

 

 

On Tue, Jun 10, 2014 at 1:17 PM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Akshay Bhatnagar
Gesendet: Dienstag, 10. Juni 2014 03:47
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Reg: movement of protein outside box

 

Hello everyone

 

I have performed a 10 ns equilibration to simulate a amino acid in a 30 A water box, but after the equilibration the amino acid has moved to the corner of the box. can anyone explain me the reason?

 

Diffusion. If you wan’t to have it in the middle of the box, see in VMD “pbc wrap –all –compound res –center com –centersel protein”. Please notice that the

Center of the box can be everywhere you want.

 

Also can anyone tell me the exact difference between equilibration and production run? If I use pressure control parameter in equilibration then is it equivalent to production run?

 

During equilibration you usually have: restraints, temperature control, pressure control … (see NVT,NPT)

During production run you usually have no external controls of your simulation. (see NVE)

 

Thank you very much

With Regards

Akshay Bhatnagar

PhD Student

BITS Pilani Hyderabad Campus

 

 

 

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