Hi, Maybe it's a good idea to have ld-seed=-1 as a default if that's not already the case. Ran.
Berk Hess wrote: > Hi, > > I don't know why I did not add checks for ld-seed before. > Now grompp gives a note when continutation=yes and ld-seed!=-1. > > tpbconv will now generate a new ld-seed when reading a trajectory > (but you should not use tpbconv, use a checkpoint file instead). > > But yesterday I forgot to tell that there is a bug in the checkpointing > of mdrun in 4.0 - 4.0.3. Without domain decomposition the initial box > size would always be stored in the checkpoint file, which causes problems > with NPT simulations. NPT simulations with domain decomposition and > all NVT simulations were fine. > > Gromacs 4.0.4 will all bugs fixed and extra checks should be released > today. > > Berk > > > Date: Wed, 4 Feb 2009 19:30:47 -0500 > > From: chris.ne...@utoronto.ca > > To: gmx-users@gromacs.org > > Subject: [gmx-users] micelle disaggregated in serial, but not > parallel, runs using sd integrator > > > > It appears as if you were correct Berk. I will report on the results > of my 24h test tomorrow, but I also set up another system > > that used ld_seed=1993 and ran in 20 ps segments instead of the 200 > ps segments that I was previously using. This system shows > > signs of disaggregation on the 200 ps time-scale as opposed to the 2 > ns time-scale that I observed for 200 ps segments. > > > > I don't know how you figured that one out, but I am very grateful. > > > > Now that I see the trajectories, it does make sense that any net > movement applied to an individual molecule by the noise will > > lead to directed movement over many separate segments. > > > > I think this is probably worth a note in the grompp output for sd > runs when a user sets ld_seed to something other than -1 and > > utilizes the -t option (or some other indication that this is > intended as a continuation). > > > > Chris. > > > > -- original message -- > > > > Thank you Berk, > > > > I will repeat my runs using the checkpoint file and report my > findings back to this list. Thank you for this advice. > > > > Chris. > > > > -- original message -- > > > > Hi, > > > > In this manner you use the same random seed and thus noise for all > parts. > > In most cases this will not lead to serious artifacts with SD, > > but you can never be sure. > > When checkpoints are used, you do not repeat random numbers. > > This also gives a difference between serial and parallel in 4.0. > > With serial you get exactly the same noise per atom, in parallel not, > > since atoms migrate from one node to another (with domain decompostion). > > > > If you do not use checkpoints, use ld_seed=-1 and do not use tpbconv. > > > > Berk > > > > > > _______________________________________________ > > 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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ------------------------------------------------------------------------ > Express yourself instantly with MSN Messenger! MSN Messenger > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > ------------------------------------------------------------------------ > > _______________________________________________ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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