回复： Re: [gmx-users] how to remd analysi?

[Mark Abraham]

xi zhao wrote:
>  I performed remd using GROMACS 3.3.1 at four different temperatures: 
> 270k, 400k, 540k, 660k, and produced four trajectories. I want to know 
> whether my simulation is ok, but I do not know how to analysis my 
> trajectories.

Probably these temperatures are spaced far too widely if you are not
doing a vacuum simulation of a small peptide. Check literature for more
suitable temperature ranges.

> Though I have demux.pl script and produced 
> replica_index.xvg and replica_temp.xvg files, the contents of two files 
> are the same! 

I'm not familiar with the contents of theses files, but if your
temperatures are too widely spaced, you won't see exchanges, and that
might be the reason for these files being identical.

> I use trjcat_d to produce a continuous 
> trajectory,according to wiki gromacs. In fact,  for a REMD 
> simulation, I can not judge whether the simulations is ok , and if they 
> are ok, how to further analyze or  extract useful information from 
> trajectories! Are you clear?

This question is common to all other MD simulations, and the answer to
it depends on the purpose for the calculations. To get some ideas, have
a look at the literature for similar calculations, do background reading
and be prepared to think hard.

Mark