<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:10pt"><div><br><br>Thanks for your reply.<br>So if I have to simulate the system at T=323 K , I need to set <font size="3"><span style="font-weight: bold;">both</span></font> ref-temp and gen-temp <font style="font-weight: bold;" size="3">at 323K</font>. Right? I guess no difference between two items , I mean ref and gen, to be set at what temperature!<br><br></div><div>Sincerely,<br>Shima<br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 10pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Shima Arasteh <shima_arasteh2001@yahoo.com>; Discussion
list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, June 10, 2012 4:24 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Temperature in NVT file<br> </font> </div> <br>
<br><br>On 6/10/12 7:46 AM, Shima Arasteh wrote:<br>> <br>> Dear gmx users,<br>> If i want to simulate the system in Temperature=323 k , am I supposed to change<br>> the ref-t or gen-t in NVT file?<br>> <br><br>Both. The gen_temp parameter generates the velocities according to a Maxwell distribution. The ref_t parameter is what the thermostat tries to maintain. If you generate velocities at some temperature other than what you're trying to equilibrate, the thermostat may have trouble and the simulation may crash. Perhaps you'd get lucky, but there's no reason to risk it by doing something nonsensical.<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul, Ph.D.<br>Research Scientist<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540)
231-9080<br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br><br>========================================<br><br><br> </div> </div> </div></body></html>