Re: [gmx-users] position restrain energy

On 4/19/16 9:57 AM, Nikhil Maroli wrote: reference previous mail thread : https://www.mail-archive.com/gromacs.org_gmx-users%40maillist.sys.kth.se/msg18799.html Dear Justin, Thanks ,so i have to define restrain for individual molecules.in that case how should i define *mdp file ,since eight re

Re: [gmx-users] position restrain energy

reference previous mail thread : https://www.mail-archive.com/gromacs.org_gmx-users%40maillist.sys.kth.se/msg18799.html Dear Justin, Thanks ,so i have to define restrain for individual molecules.in that case how should i define *mdp file ,since eight restrains are there for each ring A,B,C,D,E,F,G

Re: [gmx-users] position restrain energy

On 4/18/16 9:05 AM, Nikhil Maroli wrote: Hi thanks for your suggestion, When i give both same name in mdp and top it gives an error Atom index (123) in position_restraints out of bounds (1-122). This probably means that you have inserted topology section "position_restraints this is my topo

Re: [gmx-users] position restrain energy

Hi thanks for your suggestion, When i give both same name in mdp and top it gives an error Atom index (123) in position_restraints out of bounds (1-122). This probably means that you have inserted topology section "position_restraints this is my topology file structure ; Include forcefield para

Re: [gmx-users] position restrain energy

You defined in .top file as POSRES_Protein so in .mdp file you should call as define = -DPOSRES_Protein. The names in .top and .mdp should match On 18 Apr 2016, at 08:46, Nikhil Maroli wrote: > > Dear all, > i wanted to include position restrain to cyclic peptide nanotube c-alpha > atoms

[gmx-users] position restrain energy

Dear all, i wanted to include position restrain to cyclic peptide nanotube c-alpha atoms,i have generated posre_cpn.itp file and added define = -DPOSRES in mdp file. and added in .top as #ifdef POSRES_Protein #include "posre_cpn.itp" #endif when i check with gmx energy i couldnt find an