<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">><b><span style="font-weight: bold;">From:</span></b> Chih-Ying Lin <chihying2008@gmail.com><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">><font face="Tahoma" size="2"><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight: bold;"></span></b></font>><font face="Tahoma" size="2"><b><span style="font-weight: bold;">Sent:</span></b> Quarta-feira, 3 de Novembro de 2010 0:10:47<br><b><span style="font-weight: bold;"></span></b></font>><font face="Tahoma" size="2"><b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP
?<br></font>><br>><br>><br>>Hi<br>>I read some papers and many simulations were performed under high temperature to induce the unfolded protein. <br>>However, the authors did not mention how they conducted the simulations under high temperature, 498 K. <br>
>They did not mention which NVT or NPT were adopted for such high temperature.<br>>None of any parameters about the temperature coupling and pressure coupling were described on the papers.<br>><br><br><span> Hello Lin, do you know this article? <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555740/">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555740/</a></span><br> It's simple and has a fairly detailed section of the high temperature methods. It should be a good start.<br><br>><br>>Are there any standard procedures to perform High temperature - MD simulation?<br>
>Where can I find the standard procedures?<br><br> 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 <br> pressure even at 498K, I'll search my files for the article that reviews this stuff. <br> What water model are you using?<br><br>><br>>At 498K, protein is cooked.<br>>Under NPT, the water evaporated. => so, turn on pressure coupling with a (very) high pressure to keep the water molecules.<br>>Under NVT, the pressure increased dramatically.<br>
>So, to run MD simulations under the high temperature means to run the MD simulation under high pressure at the same time?<br>><br>><br>><br>>But, I did read one paper that the authors performed the MD simulation under high temperature and high pressures separately <br>
>and further discuss the effect the high temperature and the high pressures on protein separately.<br>><br>><br>><br>>Thank you<br>>Lin<br>><br><br>Ricardo.<br><br><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 8pt;" lang="PT-BR">---</span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 8pt;" lang="PT-BR"> <font size="1"> </font></span></p><font size="1">Ricardo O. S. Soares , PhD Student.<br>Group of Biological Physics - Department of Physics & Chemistry<br>Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.<br>Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil.<br>Phone: +55 16 36024840.</font> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><br><span style="font-size: 8pt;" lang="PT-BR"><a rel="nofollow">Curriculum
Lattes:</a></span><a rel="nofollow"><span class="texto"> <font size="1">http://lattes.cnpq.br/0777038258459931</font></span></a></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 8pt;" lang="PT-BR"><a rel="nofollow">ross_usp@yahoo.com.br</a>,<a rel="nofollow">rsoares@fcfrp.usp.br</a></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 8pt;" lang="PT-BR"> <br></span></p><br>
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