----- Original Message ----- From: Dmitri Dubov <ddu...@ngs.ru> Date: Thursday, August 26, 2010 18:17 Subject: Re[2]: [gmx-users] initial velocities analysis To: Discussion list for GROMACS users <gmx-users@gromacs.org>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Re[2]: [gmx-users] initial velocities analysis <!-- body { margin: 5px 5px 5px 5px; background-color: #ffffff; } /* ========== Text Styles ========== */ hr { color: #000000} body, table /* Normal text */ { font-size: 9pt; font-family: 'Courier New'; font-style: normal; font-weight: normal; color: #000000; text-decoration: none; } span.rvts1 /* Heading */ { font-size: 10pt; font-family: 'Arial'; font-weight: bold; color: #0000ff; } span.rvts2 /* Subheading */ { font-size: 10pt; font-family: 'Arial'; font-weight: bold; color: #000080; } span.rvts3 /* Keywords */ { font-size: 10pt; font-family: 'Arial'; font-style: italic; color: #800000; } a.rvts4, span.rvts4 /* Jump 1 */ { font-size: 10pt; font-family: 'Arial'; color: #008000; text-decoration: underline; } a.rvts5, span.rvts5 /* Jump 2 */ { font-size: 10pt; font-family: 'Arial'; color: #008000; text-decoration: underline; } span.rvts6 { font-weight: bold; color: #800000; } span.rvts7 { font-weight: bold; color: #800080; } a.rvts8, span.rvts8 { color: #0000ff; text-decoration: underline; } span.rvts9 { font-weight: bold; color: #800080; } span.rvts10 { font-size: 8pt; font-family: 'arial'; font-style: italic; color: #c0c0c0; } a.rvts11, span.rvts11 { font-size: 8pt; font-family: 'arial'; color: #0000ff; text-decoration: underline; } /* ========== Para Styles ========== */ p,ul,ol /* Paragraph Style */ { text-align: left; text-indent: 0px; padding: 0px 0px 0px 0px; margin: 0px 0px 0px 0px; } .rvps1 /* Centered */ { text-align: center; } --> ----------------------------------------------------------- | > Hi, Justin. > I'm also interested in this question. Could you make clear: > > Anna Marabotti wrote: ... >> - is there a way to check for the velocities or for the random seed >> used? I had a look at the .log file but I didn't find the information. >> g_traj generated a very big file, and presently I have some problems to >> analyze it. How can I see initial velocities? >> ... > In other words, when gen_seed is set to -1, there is a rigorous rule for seed > calculation. How can I get the value of this seed? I need it to repeat > exactly the same run, e.g., with more detailed outputs. See manual 7.3.17, and inspect your mdrun .log file for the value grompp actually used. However, note http://www.gromacs.org/Documentation/Terminology/Reproducibility Mark | -----------------------------------------------------------
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