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Hi,<br><br>Everything depends completely on how much drift you are talking about.<br>There will always be energy drift, it is just a question how much.<br>In general shifted potentials will be cheaper (and lead to less energy drift)<br>than setting nstlist to 1, but for most purposes a bit of energy drift is no problem.<br><br>Berk<br><br>> Date: Thu, 12 Mar 2009 10:55:47 +0100<br>> From: degaetani@dcci.unipi.it<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Re: Energy Drift in Gromacs 4.0<br>> <br>> Even if a system is not well equilibrated (but not so far from <br>> equilibrium) ,energy should be conserved in NVE ensemble.<br>> Try to lower the nstlist from 10 to 1 i.e. renew every time the <br>> neighbourlist. In systems I have studied, that is the key that improve <br>> much more energy conservation. It works even without switching of VdW <br>> potential.<br>> <br>> Luca Dre Gaetani<br>> ><br>> > Message: 1<br>> > Date: Thu, 12 Mar 2009 13:59:11 +1100<br>> > From: Mark Abraham <Mark.Abraham@anu.edu.au><br>> > Subject: Re: [gmx-users] Re: Energy Drift in Gromacs 4.0<br>> > To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> > Message-ID: <49B87A7F.30807@anu.edu.au><br>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>> ><br>> > Ilya Chorny wrote:<br>> > <br>> >> If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE <br>> >> simulation they should counter balance. I am leaking K.E. somewhere. I <br>> >> reran with a relaxed P.E(t) and saw the same behavior. This is <br>> >> happening both at 2 and 4 fs so its not a time step issue. Any thoughts? <br>> >> I thought it might be COM removal so I turned it off to no avail. <br>> >> <br>> ><br>> > "going down" is seriously unhelpful. I told you you needed to <br>> > equilibrate before measuring such things. If you want people to take <br>> > your problem seriously, you'll need to announce that you have <br>> > equilibrated and for how long and in what ensembles, etc. If you're <br>> > having a problem, you need to demonstrate what areas you feel are not <br>> > causing it. We're not your family doctor who will ask a pile of <br>> > questions to find out the problem :-)<br>> ><br>> > Mark<br>> > <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search 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<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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