Re: [AMBER-Developers] ntb vs ifbox?

From: Yong Duan <>
Date: Wed, 07 Dec 2011 08:32:19 -0800

Huh, I mis-read, thought "= 6" meant "= 7" and "6" was a typo. It's not,
but the "4-7" should be changed to "4-6" in the paragraph above. So, "7"
is a typo, instead :).

In the code "netCDF" read is controlled by ntx = 8,9.

Can I propose a "ntx = 0" option? That is, it depends on the availability
of the information in inpcrd (and potentially make this as the default?).

For ntx = 0, velocities are read from inpcrd, if available. The velocities
in inpcrd will be used as the starting V if irest = 1 (or 0??).

If irest = (the value that says not to use the V), velocities will be
re-assigned. The manual says irest=0 = "No effect". I always thought that
irest=0 meant reassign the velocities.

If velocity information is unavailable in inpcrd, then, depending on
irest, if irest = 1, it probably should quit. If irest = ("do whatever you
want") or ("reassign"), re-assign the velocities.

Since the box information is always read in formatted inpcrd when ntb > 0,
it might be more consistent to have the same behavior for unformatted and
netCDF read (I think formatted and netCDF already behave like this, not
sure about unformatted).

To realize above logic, we need to add a global logic variable to indicate
whether or not the velocities have been read from inpcrd. For
completeness, it might be a good idea to add a global logical variable to
indicate whether or not the box information has been read (is this already
the case??).

Am I driving everybody nuts? Sorry :)).

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 12/7/11 4:55 AM, "David A Case" <> wrote:
>On Tue, Dec 06, 2011, Yong Duan wrote:
>> Another thing that I often feel somewhat confusing is the ntx. I think
>> manual and behavior are actually inconsistent.
>I wonder if you are looking at an old version of the manual(?)  ntx=7 is
>no longer listed as an option.  But please, fix typos and reword things
>to make them better.
>> If above is true, ntx's function is pretty much limited to reading the
>> velocities (and formatted/netCDF restart files).
>Note that "unformatted" does not mean "netCDF".  I'm not sure what Dan
>has in
>mind for this, but we/he should get this functionality installed in the
>as soon as possible.
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Received on Wed Dec 07 2011 - 09:00:02 PST
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