Dear Mark, Thank you very much for your valuable advice. Best regards, Tri
________________________________ From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Sat 3/15/2008 8:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] kinetically trapped in a local minimum??? #NGUYEN CONG TRI# wrote: > Dear Gromacs users, > > How can we know that the system is properly equilibrated or whether we > should extend the equilibration step. Someone suggest that we look at > the potential energy to see whether it has converged? Is it correct? That's one test. You should look for converged behaviour in a range of simulation observables that hopefully include those that will indicate that the observable(s) on which you plan to collect data in the production run are/will be showing equilibrated behaviour. > One more question, normally, we carry out the equilibration at 300K, > don't we? If you're interested in a room-temperature system, that would be a logical choice. If you're interested in another temperature, be aware that most force fields are not parametrized on data from other temperatures. > How can we know that this temperature is enough and the system > is not kinetically trapped in a local minimum? And if it is whether it > affects the production run later on? You can't ever tell from a single simulation in isolation. You can try a cheaper simulation at a higher-temperature or coarser-graining to get an idea how big the system space might be, or do simulated annealing (or other such nonlocal-search approaches), but there's never a guarantee that these reflect what's accessible in a dynamical system. An implicit-solvent replica-exchange MD simulation (e.g. with AMBER) can be instructive. Experience with similar systems can be a guide also. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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