[gmx-users] set up topology in free energy calculations

Maik Goette mgoette at mpi-bpc.mpg.de
Mon Apr 7 14:06:05 CEST 2008


1. Yes. I'd use version a) because of, the less dummies, the better.
2. Yes
3. Of course, charges have to vanish for dummies, too. Keep the bonded 
terms. If not, your dummies will "diffuse" away.

Yes, your assumption about dummies is right.

Actually, I won't use this system for your first perturbation. Take 
something simpler.
Second, as indicated by point 3, you will have to tackle a disappearing 
netto charge of -1 (depending on the pH of course). This usually is a 
There were discussions of PME being problematic here.
Morphing an ion to counter that charge difference is possible. However, 
I think this would lead to a very bad equilibrated system and no 
reasonable results.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

friendli wrote:
> Dear Gmx users,
> I am calculating the mutation free energy from amino acid Asp to Asn as 
> a test job for my practice.
> I have some questions about setting up the topology file.
> 1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or 
> simply -OH to -NH2.
> In topology, O <-> N.
> What about the hydrogens, do I need one or two dummy(DUM) atoms?
> a), DUM <-> H ; H(of OH) <-> H(of NH2)
> b), DUM <-> H(of NH2); DUM <-> H(of NH2); H(of OH) to DUM
> a) or b) should I use?
> 2, I need to provide the coordinates for the dummy atoms in the .gro 
> file(Asp), right? since otherwise the # of atoms in .top and .gro will 
> mismatch.
> 3, from the tutorial(methane) I read, the masses of the dummy atom keeps 
> like real atom and the C6 and C12 changes to zero in [atomtypes] to 
> vanish the nonbonded interactions.  How to deal with the bonds and the 
> charges for dummy atoms? bonded interactions?
> I think I am a bit confused by the definition of the dummy atom.  I 
> understanding is a dummy atom is a atoms with same mass but no 
> interaction with all other atoms. Is that right?
> thanks for help and suggestions are appreciate.
> QL
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