[gmx-users] how can we obtain replicated trajectory?

[Mark Abraham]

As you can see in your plot, no replicas from 400K got down to 300K in the
1.5ns you simulated. So you've so far derived no benefit from REMD (unless
you want sampling at lots of temperatures). Perhaps a simulation a hundred
times longer might get a few such events? You might as well have run a
simulation at 400K to see what it did... What do you hope REMD will help
you observe?

Mark

On Fri, Mar 22, 2013 at 12:28 PM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
>
>  I've finished a replica exchange simulation with 72 replica (300K-580K)
> under explicit solvent model. It generate 72 trajectory and the replica
> since to "cross" well with neighboring temperature. Here is the figure:
>
>
> http://dl.dropbox.com/u/**56271062/REMD.png<http://dl.dropbox.com/u/56271062/REMD.png>
>
>  I am just wondering how can we generate and visualize the system at 300 K
>  with that at 400-500 K? There is a ligand in my system, and it is expected
> to escape binding pocket with large loop movement....
>
> thank you very much
>
> best
> Albert
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