Dear Joao,
Thank you very much for your support. I am following Justin's tutorial but
simulating a fragment of antibody (Fab).
I will try the different water models.
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Thu,
Just one more thing. If you're following Justin's tutorial, I guess you're
using lysozyme. This protein will not deviate very much from it's crystal
structure at 27ºC, let alone at -40ºC (*in the context of a molecular
dynamics simulation**). I understand that it may be possible to
experimentally
Higher complexity water models such as TIP5P and so on are able to better
reproduce bulk water properties (please check the paper I linked in my
earlier email). However, these models require more computational effort
(due to the increased number of interactions) and may not work well in
Dear Justin,
Thank you very much. I will try the possible water models.
Do you know if there are water models to resemble frozen state?
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Thu, Jun 8, 2017 00:50 AM
To: "ZHANG
On 6/7/17 12:50 PM, ZHANG Cheng wrote:
Dear Joao,
Thank you for your help and the paper link.
I was following Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On that page, it says "spc216.gro as the solvent configuration for
Dear Joao,
Thank you for your help and the paper link.
I was following Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E,
or TIP3P water", and it outputs
Hello,
"spc216.gro" is not a water model, it's just a pre-equilibrated simulation
box (300 K and 1 bar) with the coordinates of 216 3-site water molecules.
SPC and TIP3P are two examples of 3-site water models. Water model
properties are well studied and tabled (e.g.
Dear Gromacs,
I would like to simulate the protein at subzero condition in aqueous buffer, to
see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I
ask what is the valid temperature range for water "spc216.gro" ? If I run the
simulation at -40 C, does it still assume
