On Sun, May 24, 2015 at 1:10 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> 1.) While trying to figure out what is wrong with my QM/MM calculation,
> I noticed the following. Consider the following Amber tutorial:
>
> http://ambermd.org/tutorials/basic/tutorial0/
>
> In this tutorial, concerning the 03_Production run, it states that the
> use of ntx=5 specifies that the coordinates and velocities will be read
> in from an inpcrd file. However, in the actual tutorial procedure, one
> reads in the p and q values from a .rst file. This is a minor typo, I
> believe.
>
inpcrd and restart formats are identical. The way I think about it, you
call it an "inpcrd" (INPut CooRDinate) file when you pass it to sander
using the "-c" flag. You call it a restart file when you specify it as an
output via the "-r" flag. So the same file is both an inpcrd and a rst,
depending on the context. But the fact is, they are the same format. And
that format allows them to either have or *not* have velocities (and unit
cell dimensions). [1]
>
> 2.) I noticed that, in the Amber 15 manual, the ntx keyword can only
>
> take on the values 1 or 2 (not five).
>
This is true for the PBSA program (page 75 or something). If you look in
the documentation for sander and pmemd (page ~300 or so), you'll see that
the options are 1 and 5. It is confusing to be sure, and we should make
them consistent. But 5 *is* documented :). What's not documented is the
use of ntx=7, which behaves the same as 5 to my knowledge.
HTH,
Jason
[1] As an aside, the OFF library format actually has a velocity table that
allows you to specify initial velocities. None of the standard libraries
do -- they are always set to 0. But that leads me to believe that LEaP
*can* print out inpcrd files with velocities. For whatever that's worth
:).
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun May 24 2015 - 16:00:03 PDT
