Re: [AMBER] Unable to view the box coordinates in VMD

From: Ramin Salimi <>
Date: Mon, 22 May 2017 05:51:55 +0000

Dr. Case

Thanks so much for your reply.

I have two more questions:

Is there any such possibility that we make a specific set of three dimensions for the box with a specific number N of water molecules when we are working in Leap trying to make .prmtop, and .inpcrd files? For example, I wanna make 13000 water molecules in a 70*70*70A0 box. Do we have any such capability?

Is there any way other than the buffer size in leap to manipulate the box dimensions, and the number of water molecules?

Because when I stretch my molecule, it is stretched along the principal axis so the dimensions of the box should be quite different, but how much control do we have over determining the box dimensions?



From: David Case <>
Sent: Sunday, May 21, 2017 6:23:54 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Unable to view the box coordinates in VMD

On Sun, May 21, 2017, Ramin Salimi wrote:

> I have a .mdcrd trajectory file that I converted to .nc format using cpptraj.

> When I load my trajectory file with .nc format, and choose Amber
> coordinate with periodic box as its type, it doesn't visualize the
> system in vmd giving the following message:
> Using plugin crdbox for coordinates from file

This is expected: for VMD, "Amber coordinates w/ periodic box" means the
old, ASCII format.

> And when I choose the NetCDF(Amber, MMTK) option, it shows the solution
> but doesn't show the box.

I don't have any input here: maybe others on the list can chime in, or
you can ask for help from the VMD people. If you image the trajectory in
cpptraj before saving the file, you can see the extent of the solvent easily,
even if the box outline itself is not visible.

> One more question is that if I change the dimensions from the end of
> the inpcrd file, and then continue with minimization, heating, and
> equilibration, are the new dimensions going to be scaled back to the
> original ones by the end of equilibration?

Depends on the value of ntp. If you run constant-pressure simulations,
the dimensions of the box are adjusted to be approrpriate for the pressure you
choose (1 atm by default). So, if you perturb the box dimensions, they
will tend to return to earlier values. If you request a constant volume
simulation, the box sizes won't change (but you then won't have the
appropriate numbers of water molecules for the new box size.)


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