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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Wed, 12 Mar 2008 12:31:12 +0100<br>> From: andreas.frank@ch.tum.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Re: DMSO G53a6 FF in Gromacs<br>> <br>> Hi Berk,<br>> <br>> Thanks for replying so quick. I made it rigid in that way that I used <br>> bonded interactions also for the groups that are not directly connected <br>> (FF parameters gb_49 & gb_50) and then applied all-bond SHAKE. For the <br>> other bonds I used gb_41, gb42 and for the three angles ga_45 and ga_46.<br>> <br>> Andreas<br><br>There could be another issue.<br>With reaction-field you always introduce integration errors.<br>With water this leads to a temperature of 305 K when Berendsen coupling<br>to 300 K with tau_t=0.1 ps and the Gromos cut-off setup.<br><br>In Gromos there is/was a problem with inconsistent ways of determining<br>the temperature. Therefore the effective temperature in the simulation<br>can be several degrees higher than the one reported in the paper.<br><br>What coupling method did you use and what is your real temperature?<br><br>Berk.<br><br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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