Res: [gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?

[Ricardo O. S. Soares]

>From: Chih-Ying Lin <chihying2008 at gmail.com>

>To: gmx-users at gromacs.org
>Sent: Quarta-feira, 3 de Novembro de 2010 0:10:47
>Subject: [gmx-users] Standard Procedures to perform MD under High Temperature 
>498 K, either NVT or NTP ?
>
>
>
>Hi
>I read some papers and many simulations were performed under high temperature to 
>induce the unfolded protein.  
>
>However, the authors did not mention how they conducted the simulations under 
>high temperature, 498 K. 
>
>They did not mention which NVT or NPT were adopted for such high temperature.
>None of any parameters about the temperature coupling and pressure coupling were 
>described on the papers.
>

    Hello Lin, do you know this article? 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555740/
    It's simple and has a fairly detailed section of the high temperature 
methods. It should be a good start.

>
>Are there any standard procedures to perform High temperature - MD simulation?
>Where can I find the standard procedures?

    I think one of the main issues you have to mind in a high T MD, is the 
explicit solvent. It is possible to mantain the water liquid under a normal   

    pressure even at 498K, I'll search my files for the article that reviews 
this stuff. 

    What water model are you using?

>
>At 498K, protein is cooked.
>Under NPT, the water evaporated. => so,   turn on pressure coupling with a 
>(very) high pressure to keep the water molecules.
>Under NVT, the pressure increased dramatically.
>So, to run MD simulations under the high temperature means to run the MD 
>simulation under high pressure at the same time?
>
>
>
>But, I did read one paper that the authors performed the MD simulation under 
>high temperature and high pressures separately 
>
>and further discuss the effect the high temperature and the high pressures on 
>protein separately.
>
>
>
>Thank you
>Lin
>

Ricardo.


---
 Ricardo O. S. Soares , PhD Student.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.
Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo,  Brazil.
Phone: +55 16 36024840. 

Curriculum Lattes:http://lattes.cnpq.br/0777038258459931
ross_usp at yahoo.com.br,rsoares at fcfrp.usp.br


      
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