Re: [AMBER-Developers] ntb vs ifbox?

From: Yong Duan <>
Date: Tue, 06 Dec 2011 09:06:52 -0800

Jason and Ben,

Forcing users to edit prmtop is of course a bad idea.

But, for the very few who wants to use ntb=0 for systems of ifbox=1 (or
ntb=1 for ifbox=0), they'd better know what they are doing. If a first
year grad student does that, it is extremely likely an error. For those
well-trained and highly innovative minds, editing prmtop is a piece of
cake. If not, they probably should stay away from inventing new chemistry.

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 12/6/11 7:08 AM, "Ben Roberts" <> 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
>>   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
>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.
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Received on Tue Dec 06 2011 - 09:30:03 PST
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