[gmx-users] problems with rerun

Hi I have a molecule described by two sets of parameters (in atom connectivity and coupe values of bond interactions) and I need to get the energy difference between those two descriptions. I have been having problems with the rerun capability (I am using the latest version of gromacs) I did the

Re: [gmx-users] problems with rerun

ould be a sensible combination for these? Thanks so much for your help, I think I have a better idea of what I'm doing wrong. > rsf wrote: >> Hi I have a molecule described by two sets of parameters (in atom >> connectivity and coupe values of bond interactions) and I

[gmx-users] (no subject)

Hi I want to describe a reaction for what I have a system described by two different connectivities and need to run an MD calculation on a mapping potential of the type V1- C (V2-V1), where V1 and V2 are my diagonal elements of the evb matrix and C is a parameter. Does gromacs have support for run

[gmx-users] EVB and mapping potentials

Hi I want to describe a reaction for what I have a system described by two different connectivities and need to run an MD calculation on a mapping potential of the type V1- C (V2-V1), where V1 and V2 are my diagonal elements of the evb matrix and C is a parameter. Does gromacs have support for ru

[gmx-users] EVB and mapping potentials

Hi I want to describe a reaction for what I have a system described by two different connectivities and need to run an MD calculation on a mapping potential of the type V1- C (V2-V1), where V1 and V2 are my diagonal elements of the evb matrix and C is a parameter. Does gromacs have support for

Re: [gmx-users] RE: evb and mapping potentials

(charges, bonds, angles, dihedrals) as well as connectivities that describe the chemically active part of the system. Thanks so much for your comments. Romelia > >>6. EVB and mapping potentials (rsf) >> > > Hi, > > I do not understand your question, but what you try to

[gmx-users] (no subject)

Hi I have a silly question about the implementation of the Gromos forcefield in gromacs, particularly about the exclusions. I have the gromos manual and have seen that, for instance, for the residue MET there are only 1st and 2nd neighbors exclusions defined for it. However, when I build a protei