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Pedro Lacerda

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08/07/2016

03:58 PM GROMACS Feature #1929: gmx solvate only updates topology when the solvent is "SOL"
Something like the following non-working patch may do the job. The solvent name is hard-coded in solvate.cpp. Simply ...

07/20/2013

11:46 PM GROMACS Feature #1307: PDB files should be written with the element symbol column
Okay, I see.. anyway i just made a commit using atom.elem or atom.atomatomnumber to get this info. You can just ignor...
09:25 AM GROMACS Feature #1307: PDB files should be written with the element symbol column
The logic of my last sentence don't works, but I guess that t_atom's elem is really always empty before fprintf ATOM ...
09:10 AM GROMACS Feature #1307: PDB files should be written with the element symbol column
Yes, we can't solve this issue for e.g. GRO since doesn't have a field for element, just atom names.
But I guess t...

07/19/2013

10:54 PM GROMACS Feature #1307 (Closed): PDB files should be written with the element symbol column
Generally it isn't a problem. But for molecules like FMNO from G53a6 where atom names starts with 'F', VMD sets the e...

06/13/2013

09:45 AM GROMACS Revision 57438bd2: Fix genion -nq and -pq when using -neutral
Currently genion can't neutralize (-neutral) systems when -nq/-pq
differs from -1/+1. This commit fixes the problem.
...
09:45 AM GROMACS Revision c07f5f5f: Fix -neutral option in genion
The help for -neutral says that it "will add enough ions to neutralize
the system", but this option can only be used ...
04:47 AM GROMACS Bug #1213: GMXRC make dubious assumptions
Christoph Junghans wrote:
>
> ...

06/10/2013

11:11 PM GROMACS Bug #1278: Wrong topology update after genbox solvation
Oliver, you can refer to these waters using their residue id. I don't know why pdb2gmx generated these names. I hope ...

06/07/2013

10:32 AM GROMACS Revision 71df8733: Add a GMX_NO_CREDITS variable to not show credits
It's annoying to get output loaded of credits messages, especially when
running scripts. This commit add GMX_NO_CREDI...

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