Re: [AMBER] Particle insertion and deletion

From: Roman Osman <>
Date: Sun, 14 Mar 2010 17:12:25 -0400

I think this is not the right approach; you need to use a grand
canonical ensemble in which the number of particles is not fixed.
You can do this with Monte Carlo approaches. See for example:


On Mar 14, 2010, at 4:14 PM, Dian Jiao wrote:

> Hello,
> I was trying to analyze the energy by inserting a particle or
> deleting a
> particle from an existing trajectory.
> 1. Insertion
> I have run simulation with a box of water and wanted to insert a
> particle
> with random position and orientation to each frame and reevaluate the
> energies. How do I do that? Do I need to generate new trajectory
> with the
> particle and also new prmtop for each frame and analyze it?
> 2. Deletion
> I know how to delete a particle from a trajectory with "STRIP"
> command. But
> again, how to generate new prmtop (w/o the particle) from the old
> prmtop?
> I thought I could do it this way: pick one frame from the simulation
> trajectory of a waterbox with the particle and manually remove the
> particle
> from the pdb. Then use antechamber to generate the mol2 and leap to
> create
> prmtop and inpcrd. As it turned out, the antechamber didn't work,
> couldn't
> generate the mol2 for waterbox, because of the "cannot run
> bondtype.....properly".
> Does anyone know a better way to handle this?
> Thanks in advance.
> ~Dian
> _______________________________________________
> AMBER mailing list

Roman Osman

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Received on Sun Mar 14 2010 - 14:30:03 PDT
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