[gmx-users] Difference in hydrogen bonds between different softwares

Mark Abraham Mark.Abraham at anu.edu.au
Sat Oct 29 12:40:40 CEST 2011

On 29/10/2011 9:22 PM, larif sofiene wrote:
> Greeting
> I'm doing a MD simulation of a monomeric protein and i got different 
> results about hydrogen bonding from what another team has found (they 
> use other MD software ) , for example i find a Hydrogen bound between 
> K 77 - Asp 81 and they find K 77 - R 82, my question is :
> Is hydrogen bounding different from one simulation to another (with 
> the same running time) and if not are hey different from one software 
> to another ?
> If so, when publishing results is it scientifically credible to 
> publish value that are different arguing that internal gromacs 
> mechanism of computation are different then their home-built software?

You cannot make any assertion until you can demonstrate that one of the 
simulations has converged sampling, such that such an observation is 
demonstrably not an artefact of the initial conditions.


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