Re: [AMBER] Fix dimension of the box throughout the MD simulations

From: David A Case <>
Date: Mon, 16 May 2016 14:50:49 -0400

On Mon, May 16, 2016, Iqbal, Muhammad Sajid wrote:
> I have conducted the simulations following the tutorial B1 - Section 5 with
> ntb = 1 and igb = 0. I also specify the box dimensions using the following
> command.
> set mybox box {300.092, 300.141, 300.087}

First, note that this is very different from how the tutorial sets the box
size, which is done inside the "solvateOct" command. So you are doing
something very unusual, yet you have not given us information about how
you built the system (did you use *both* solvateOct and set ... box?)

Second, the only mdin input you have specified used ntb=0. You say above
that you are now setting ntb=1, but there might be other problems with the
input that you are not seeing, and which we cannot know about either.

Try running a sample simulation without the "set mybox box" command above,
and verify that the box dimension is not changing. If that works, but
what you want to do does not work, please post both your scripts and
your scripts...these are short, yet may provide valuable clues. I'm
still guessing (based on very little evidence, to be sure) that there is some
mismatch between how you built the system in LEaP, and how you are trying
to run it with MD.

It would probably be helpful to indicate why you wish to use the above
command, i.e. what sort of simulation you have in mind.


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Received on Mon May 16 2016 - 12:00:03 PDT
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