AW: Reg: movement of protein outside box

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jun 10 2014 - 02:47:32 CDT

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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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