From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Dec 07 2011 - 06:54:01 CST
Hi John,
The problem with your setup, I suspect, is that hydrogens H4 and H5
share two parent atoms (C2 and C3), so they belong to two different
hydrogen groups (or one group containing two heavy atoms).
Here are two options:
1) duplicate atoms H4 and H5
2) make things simpler: define separate, complete topologies for both
molecules, and enforce two distance restraints linking heavy atoms
that you want to keep superimposed during the FEP transformation (see
collective variables in the user's guide). Thanks to the restraints,
this should be numerically just as efficient as the version with
shared atoms.
Also, your files indicate that you are modeling ethanol rather than methanol.
Cheers,
Jerome
On 7 December 2011 12:38, John Baker <pcxjb3_at_nottingham.ac.uk> wrote:
> Hello,
>
> I have been using NAMD for a while, but I have recently began using the FEP
> module to measure free energy differences of molecules in solvents.
>
> I am looking at the alchemical transformation of methanol --> ethane in
> water.
>
> The problem I am having is that the methanol carbon changes charge from
> 0.265 to 0, and therefore I need to include three carbon atoms.
> I placed two carbon atoms in the pdb with the same coordinates, but with
> different charges (C2, C3).
>
> Below is the PDB and PSF for the transformation in a vacuum.
>
> ATOM 1 C1 LIG 1 0.000 0.000 0.000 1.00 0.00 C
> ATOM 2 C2 LIG 1 0.000 0.000 1.530 1.00 0.00 C
> ATOM 3 H1 LIG 1 1.026 0.000 -0.373 1.00 0.00 H
> ATOM 4 H2 LIG 1 -0.512 0.888 -0.373 1.00 0.00 H
> ATOM 5 H3 LIG 1 -0.513 -0.888 -0.373 1.00 0.00 H
> ATOM 6 H4 LIG 1 0.513 0.888 1.903 1.00 0.00 H
> ATOM 7 H5 LIG 1 0.512 -0.888 1.903 1.00 0.00 H
> ATOM 8 O1 LIG 1 -1.344 0.000 2.019 1.00 0.00 O
> ATOM 9 H6 LIG 1 -1.677 0.019 2.919 1.00 0.00 H
> ATOM 10 C3 LIG 1 0.000 0.000 1.530 1.00 0.00 H
> ATOM 11 H7 LIG 1 -1.025 0.000 1.903 1.00 0.00 H
> END
>
> 11 !NATOM
> 1 O1 1 LIG C1 CR 0.000000 12.0110 0
> 2 O1 1 LIG C2 CR 0.265000 12.0110 0
> 3 O1 1 LIG H1 HCMM 0.000000 1.0079 0
> 4 O1 1 LIG H2 HCMM 0.000000 1.0079 0
> 5 O1 1 LIG H3 HCMM 0.000000 1.0079 0
> 6 O1 1 LIG H4 HCMM 0.000000 1.0079 0
> 7 O1 1 LIG H5 HCMM 0.000000 1.0079 0
> 8 O1 1 LIG O1 OR -0.700000 15.9994 0
> 9 O1 1 LIG H6 HOR 0.435000 1.0079 0
> 10 O1 1 LIG C3 CR 0.000000 12.0110 0
> 11 O1 1 LIG H7 HCMM 0.000000 1.0079 0
>
> 12 !NBOND: bonds
> 1 2 2 6 2 7 2 8
> 3 1 4 1 5 1 8 9
> 10 1 10 6 10 7 10 11
>
> When I run the simulation I receive an error of bad hydrogen group size on
> atom 2, although atom 2 is the methanol carbon and is connected to 1C, H4,
> H5 and O1.
>
> Please advise, I can't see anything wrong with the hydrogen counts.
>
> Many thanks in advance,
> John Baker (PhD candidate, University of Nottingham)
>
>
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