[gmx-users] reference simulations?

Arvid Soderhall arvid at fmp-berlin.de
Wed Mar 31 09:02:01 CEST 2004

Dear all 
I have a question concerning "reference simulations". My problem is the
following: I have produced a trajectory with a dppc bilayer (128 lipids)
and some extra small peptides and I would like to compare this
trajectory with a trajectory from a simulation of a clean dppc bilayer.
In order to produce the reference trajectory fast, I would like to use a
timestep of 5 fs (in the dppc/peptide simulaton I had to use 2 fs since
the peptides contains some explict hydrogens that are unstable using a
longer timestep) and it would be nice if it is enough to simulate only
64 lipids in stead of 128. 

What is your gut feeling about this? Can one compare two simulations
where one simulation has 128 DPPC lipids, 2 peptides, water, 2 fs
timestep, and the other 64 lipids, water and 5 fs timestep? 
Thanx in advance,


Arvid Soederhaell, PhD                              
Forschungsinstitut fuer Molekulare Pharmakologie    
Robert-Roessle-Strasse 10                           
131 25 Berlin                                       

Cell:+49-160-9835 8282 
(Cell, Sweden:+46-70-723 33 63)

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