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-- Yong Duan, Ph.D, Professor UC Davis Genome Center and Department of Biomedical Engineering University of California at Davis Davis, CA 95616 530-754-7632 On 12/6/11 7:08 AM, "Ben Roberts" <ben.roberts.geek.nz> wrote: > >On 4/12/2011, at 9:13 p.m., case wrote: > >> On Sun, Dec 04, 2011, Yong Duan wrote: >>> >>> It's so easy to mess up now. If one accidentally sets wrong ntp, you'd >>> have to restart. >> >> Did you mean "ntb" here? I don't know how to prevent people from having >> to set the correct value for ntp. >> >> I think the "ntb" variable is redundant, since its proper value can be >> determined by examining IFBOX and ntp. Keeping in mind backwards >> compatability the best approach I see is this: >> >> 1. Calculate ntb from IFBOX and ntp; >> 2. Exit with an error message if the user's input ntb is different from >> that calculated. >> 3. Update as many of the example scripts and tutorials as we can to >>avoid >> using ntb at all. > >I would agree with the general statement about the redundancy of ntb; >I've never understood why it's been necessary to set both ntb and ntp. > >I also agree with Jason's earlier comments: forcing people to edit the >prmtop if they want a particular outcome is the wrong way to go about it. >I suggest it would be easier to foul up a simulation by an >almost-but-not-quite-correct prmtop file than an obviously wrong input >file. > >It seems to me that the question is whether we're better off making >people edit the code itself if they want to use a non-standard value of >ntb, or if we let them set ntb and just print out a warning or something >in the log file. > >Cheers, >Ben > > >_______________________________________________ >AMBER-Developers mailing list >AMBER-Developers.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber-developers _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Tue Dec 06 2011 - 09:30:03 PST