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Hi,<br><br>Indeed v-rescale did not work with md-vv and md-vv-avek.<br>I have fixed it for the next beta release.<br><br>Thanks for reporting this,<br><br>Berk<br><br><hr id="stopSpelling">From: mark.abraham@anu.edu.au<br>To: sht_ycw79@hotmail.com; gmx-users@gromacs.org<br>Date: Tue, 3 Aug 2010 13:21:37 +1000<br>Subject: Re: [gmx-users] md-vv and md-vv-avek with velocity-rescaling thermostat<br>CC: <br><br>The simplest explanation for your observations is that you were not running the ensembles you think you were running. Check your input .mdp files and output .log files for confirmation about the algorithms that were actually being used.<br><br>Mark<br><br>----- Original Message -----<br>From: ¾çâ¿ø <sht_ycw79@hotmail.com><br>Date: Tuesday, August 3, 2010 12:21<br>Subject: [gmx-users] md-vv and md-vv-avek with velocity-rescaling thermostat<br>To: gmx-users@gromacs.org<br><br> <span> <table><tbody><tr><td style="padding-left: 10px; padding-right: 10px; padding-top: 15
px;" id="ecxMailContainerBody"><p> <BR><div><font face="±¼¸²" size="2"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hello!</font></div> <div><font face="±¼¸²" size="2"><font size="3"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I did some simulation with a protein moleculesusing the v-rescale thermostat. First I<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ran a simulation in the NVT ensemble with md-vv intergrator , conserved <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>energy was constant , but temperature is too low or too high. <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">>
</font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Then I tried simulating the system with md-vv-avek or leap-frog intergrator ,temperature is OK, but conserved energy has drift.</font></font></div> <div><font face="±¼¸²" size="2"><font size="3"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Using nose-hoover chain, Temperature is OK and conserved energy was constant .<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>So what is going wrong ? </font></font></div> <div><font face="±¼¸²" size="2"><font size="3"></font></font><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </div> <div><font face="±¼¸²" size="2"><font size="3"><font style="font-style: n
ormal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>T</font></font><font face="±¼¸²" size="2"><font size="3">hanks in advance.<br></font></font></div><font face="±¼¸²" size="2"><font size="3"></font></font></td></tr></tbody></table></p></span> > -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search <br>> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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