Re: [AMBER] Issues in .out trying to simulat a polymer in AMBER

From: David A Case <>
Date: Wed, 25 Jun 2014 07:42:05 -0400

On Wed, Jun 25, 2014, wrote:
> I am experimenting with using amber to simulate a non-biological polymer
> (Polyethylene terephthalate in this case). The system consists of 10
> strands of polymer, each of MW ~ 4,000. I am using a periodic boundary
> (but no water molecules)

Is the system a liquid? You density (0.07 g/cc) is extremely low.

> Looking at the trajectory
> to that point gives no indication that anything has gone awry - the
> polymer bunches up nicely in the middle of the box.

This sounds pretty dangerous--at least for Amber. Running constant pressure
where there is no "solvent" to fill up the box is likely to yield very odd
results (as it looks like you have discovered.) What was the density before
you began heating to 400K? You will probably have to constuct a system with a
reasonable volume/density, and equilibrate at the desired temperature for some
time, before moving to constant pressure simulations.


AMBER mailing list
Received on Wed Jun 25 2014 - 05:00:02 PDT
Custom Search