[gmx-users] free energy (coordinates file)

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jan 8 23:41:17 CET 2012

On 7/01/2012 9:12 PM, parto haghighi wrote:
> Dear GMX users,
> I have a question about 6th gromacs tutorial.

That's not a useful description, because nobody else knows what list 
you're looking at. A URL is much better.

> I have to perform 5 steps of calculation contain:
> 1) EM-1
> 2) EM-2
> 3) NVT
> 4) NPT
> 5) Product MD
> for each Lambda value from 0 up to 1.
> I have a .gro file contains initial coordinates of my system : drg.gro
> For lambda = 0.00 I have done 5 steps (above) and its results is : 
> md0.gro (from MD-Production)
> my question is should I use md0.gro for next calculations ( lambda = 
> 0.05) or I have to apply drg.gro file again?

Surely the tutorial mentions this. In principle, it doesn't matter 
because you are running a converged simulation at each lambda. In 
practice, it probably does matter a little because you aren't. There's 
probably some cancellation of errors if you start each lambda point from 
the same structure (and you get to run all the lambda points in parallel 
if you do so).


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