[gmx-users] Re: gmx-users Digest, Vol 43, Issue 81

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 22 21:15:06 CET 2007

servaas michielssens wrote:

> Thanks for your help, I checked the perl script (amb2gmx.pl)  it should 
> work for a solvated protein. The solvend and box are converted to 
> gromacs but the box information is not converted as it should, amber 
> only defines d and 3 angels (+information in the topology that it deals 
> with a truncated octahedron), while gromacs needs 3 vectors to defines a 
> truncated octahedron and this information is only in the .gro file not 
> in the topology. The amb2gmx.pl script only copies tree values to the 
> .gro file for an truncated octahedron so gromacs thinks it is a cubic box.
> Normally the ensembles are both NTP, I can hardly believe that 
> differnces in algoritm would cause a "Constraint error in algorithm 
> Lincs at step 0" and make the simulation crash. 

Well, possibly not *if* the only material difference was the 
implementation of fixed-pressure, but as we've discussed, you've 
probably got several material differences in the algorithms that shift 
your equilibrium ensemble. Still, if your box was that wrong, then 
there's no surprise about a LINCS error.

> But I agree that this 
> procedure is not the way to go for a good simulation, the only intention 
> of this was doing a speed comparision.

Still gotta compare apples with apples, unless you're trying for a 
pre-determined conclusion :-)


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