[gmx-users] 3rd neighbor

Hi Everyone, I would like to do some changes to the non bonded parameter of GROMOS force field. Especially, I like modify the 3rd neighbor parameters. Unfortunately, I cannot find them in the ffnonbonded.itp file. I assume that the parameter in [ atomtypes ] block are taken from Table 7 (Oostenbrin

[gmx-users] REST simulation

Dear gromacs users, Recently I stumbled over following paper: T. Terakawa, T. Kameda, and S. Takada, On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS. Journal of Computational Chemistry 32 (2011) 1228-1234. The authors suggested an easy way to run this

Re: [gmx-users] REST simulation

ext file; it's > probably doable, but I don't know how. Actually, maybe some developers can > tell if it's possible. > Good luck, > > Patrick > > Le 08/12/2011 19:01, Otto Master a écrit : >> Dear gromacs users, >> >> Recently I stumbl

Re: [gmx-users] REST simulation

o write a complete stand-alone topology, which you > can then use as input to a script to do the appropriate solute parameter > scaling for each replica. Then use grompp normally on the new set of .top > files to generate a set of .tpr files that differ not only in lambda but in > t

Re: [gmx-users] REST simulation

scripting the scaling of the potential. > Ciao, > > Patrick > > Le 12/12/2011 12:56, Otto Master a écrit : > > Hi Patrick, >> Thanks a lot for your reply. Just to be sure, you create for every >> replicate a copy of the original force field, and after you manipulate

Re: [gmx-users] REST simulation

ference is that you use a different lambda value, so a > different Hamiltonian, instead of a different temperature for each replica. > Ciao, > > Patrick > > Le 13/12/2011 11:46, Otto Master a écrit : > >> Hi Patrick, >> >> thanks for your help. What I still do not un