From: Diship Srivastava (dishipsrivastava_at_gmail.com)
Date: Fri Jul 16 2021 - 11:21:42 CDT
Yeah, I neutalized the whole system using NaCl through vmd's solvate plugin
On Fri, 16 Jul 2021, 21:38 Ashkan Shekaari, <shekaari_at_email.kntu.ac.ir>
wrote:
> Dear Diship,
>
> Did you neutralize the whole system electrostatically?
>
> ---
> ,Best
> Ashkan Shekaari
> PhD Candidate in Solid State Physics
> Department of Physics
> K. N. Toosi University of Technology, Tehran, 15875-4416, Iran
> <shekaari_at_email.kntu.ac.ir>
> <https://urldefense.com/v3/__https://scholar.google.com/citations?hl=en&user=LDzbXB4AAAAJ&view_op=list_works&sortby=pubdate__;!!DZ3fjg!qKkHkZh9BGG5KdPCIffHeo2HlqfUJhvDBdF0qUpkr2Er6djHNfFoXr183XKU444fNQ$ >
>
> ------------------------------
> *From: *"Diship Srivastava" <dishipsrivastava_at_gmail.com>
> *To: *"namd-l" <namd-l_at_ks.uiuc.edu>
> *Sent: *Friday, July 16, 2021 3:21:56 PM
> *Subject: *namd-l: Constraints required for alpha helix secondary
> structure
>
> Hi,
> I have protein containing 28 mino acid residues. The protein has 4 leucine
> residues which forms 2 leucine zipper structures and whole protein adopting
> alpha helix config with several salt bridges between different residues. I
> started with a structure similar to this ( made by Avogadro) and I was able
> to get proper psf file. During equilibration with protein in water box
> whole protein loses its alpha helix config ( I measured the alpha helix
> content using alpha helix colvar) resulting in an open ended structure with
> less than 20% alpha helix content which was around 75 % in the initial
> structure.
>
> My question is what constraint do I apply to protein such that I get
> accurate description of it during equilibration and production run? Also on
> applying these constraints will it affect the PES of the system?
>
> Diship Srivastava
> JRF
> IIT (ISM) Dhanbad
> India
>
>
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST