AW: [gmx-users] Implicit Solvent

Hola Deisy, I have used the implicit solvent which is built into mdrun-openmm. It works well: but there are some setbacks: 1. As far as I know it has only been tested with the amber 99 forcefield port for mdrun-openmm. (see http://chemistry.csulb.edu/ffamber/ ) and there is no easy way to do a pos

[gmx-users] distance restraint using bond with function 2

interstingly the distance restrain works well when one chooses the bond type 2 whatever this means physically [bonds] . . . . . . 1 614 2 5,761 40 Hans -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs

applied across the > boundary. Otherwise someone else may have more ideas to help you. > > Tom > > Forwarded Message > Date: Wednesday, January 06, 2010 22:43:20 +0100 > From: Hans HEINDL > To: TJ Piggot > Cc: > Subject: simulationg a distance

Re: [gmx-users] define a new covalent bond in gromacs

100 David van der Spoel > wrote: > > > Hans HEINDL wrote: > >> mdrun-openmm does not yet support any restraints > > But gromacs does. Therefore, it seems you need to patch openmm, for which > > you probably want to contact the openmm team. > >> > >>

Re: [gmx-users] define a new covalent bond in gromacs

mdrun-openmm does not yet support any restraints Hans Am Dienstag, den 05.01.2010, 22:12 +0100 schrieb David van der Spoel: > Hans HEINDL wrote: > > Hi all, > > > > I need to restrain the distance of two atoms in my system (the distance > > is around 57 angstrom

[gmx-users] define a new covalent bond in gromacs

distance of the two atoms. (This was Peter Eastmans idea from Standford) How could we do that and where would be the best place to define (I presume the *.top file) the bond and where should the bond length and spring constant be defined? Thanks in advance Hans HEINDL University of Westminster

[gmx-users] DNA coarse grain simulation

Are there forcefield parameters available for DNA coarse grain simulations (ideally the forcefields should be compatible with the Martini cg parameters Thanks in advance Hans HEINDL -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] WG: Changing of pulling paramters during simulation

Hi, short question: can one change the pulling parameters e.gin the afm modus during the simulation (vector and or force) Hans HEINDL University of Westminster School of Biosciences ___ gmx-users mailing listgmx-users@gromacs.org http