[gmx-users] GTG to GAG with amber FF99SB force field
tsjerkw at gmail.com
Mon May 30 09:09:21 CEST 2011
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
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.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
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