Re: [AMBER] solid surface simulation in amber

From: David A Case <>
Date: Fri, 19 Aug 2016 10:54:01 -0400

On Fri, Aug 19, 2016, Neha Gandhi wrote:
> Instead of minimizing supercell, I tried to look at unit cell and check the
> minimzation.

What happened when you did this? Did you get very large vdW energies on the
first step? Does minimization work on the unit cell, but not on the

> The unit cell dimensions are correct (I checked in vmd, materials studio,
> and also tried setBox m1 centers/vdw)
> I also tried increasing the box size in each dimension by 1 A.

I'm still lost: are you starting from an actual crystal structure? How,
*exactly*, are you using VMD to decide that the unit cell dimensions are
correct? How do you know what the correct values are?

> As Bill suggested, I tried visualising the trajectory of initial structure
> versus minimzation rst file. It seems although I am holding the HAP atoms
> fixed (ntr=1, restraint weight >> 500) in the cell, the atoms are moving
> and affects the geometry.

It's very hard to follow all that might be going wrong. Try imposing ntr=1
restraints on some very simple system (doesn't even have to be periodic).
Make sure you are getting what you expect there, and then try to see if
you can spot the difference with the HAP system where restrained atoms are
moving. (Note that even with restraints, atoms will move a little bit:
I'm assuming that when you report "the atoms are moving", you mean they are
moving by many tenths of Angstroms or more.)


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Received on Fri Aug 19 2016 - 08:00:04 PDT
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