[gmx-users] GTG to GAG with amber FF99SB force field

[Tsjerk Wassenaar]

Hi Lishan,

Your mail would be a bit more readable with more structure...

Anyway, it says in the manual you can't do perturbation on the
multiplicity. That makes sense, because interpolation from 1 to 3 goes
through a whole series of rational numbers, but you can't have
non-integer periods... If you must, you first have to remove the
dihedral, i.e. bring the amplitude to 0, and then raise again to the
other function.

Cheers,

Tsjerk

On Mon, May 30, 2011 at 3:15 AM,  <yaolisha at msu.edu> wrote:
> Dear Gromacs users: I use gromacs.4-5-3 to calculate the free energy changes
> for the GTG to GAG alchemy process, where charge annihilation is performed
> first followed by soft core VDW calculation. When doing the soft core VDW
> calculation, I see this error message ?Fatal error: [ file gtg_vdw.top, line
> 314 ]: Proper Dih. multiplicity can not be perturbed 1.000000!=3.000000?.
> Line 314 has the following content ?17 16 18 24 9? The atoms with VDW radius
> and well depth changes include 20 CT 3 THR CG2 20 -0.0000 12.01 CTD 0.0
> 12.01 ; qtot 0.0439 21 HC 3 THR HG21 21 0.0000 1.008 HCD 0.0 1.008; qtot
> 0.1081 22 HC 3 THR HG22 22 0.0000 1.008 HCD 0.0 1.008; qtot 0.1723 23 HC 3
> THR HG23 23 0.0000 1.008 HCD 0.0 1.008; qtot 0.2365 24 OH 3 THR OG1 24
> -0.0000 16 OHD 0.0 16 ; qtot -0.4396 25 HO 3 THR HG1 25 0.0000 1.008 HOD 0.0
> 1.008; qtot -0.0294 Atom types CTD, HCD, OHD, HOD are defined in a separate
> file and included in the topology file. My question is how to solve this
> problem and a related question is whether the overall setup is correct.
> Best, Lishan
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands