[gmx-users] Bond lengths

Dear Users I have performed a 200 ns MD simulation of a protein and a small molecule inhibitor of 30 atoms, using GROMOS 43a1 ff and Gromacs v 5.0. Taking reference from a number of papers and similar systems, I have used LINCS algorithm to constrain all bond lengths. I have reported interactions l

[gmx-users] Catenation and sampling

Dear users and experts I have simulated a protein in water using OPLS-AA force field. Initially I performed a 5 ns simulation and then extracted frames out of it e.g. at 1ns, 2ns, 3ns etc. and then performed simulation for 100 ns of each extracted frame. Now I have five 100 ns trajectories (A.xtc,

[gmx-users] amino acid topology

Hello users and experts I want to know if I can use gmx x2top for generating topology of a modified amino acid linked with a natural peptide sequence? or in general topology of a small molecule? Thank You Suniba -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 125

*Hi all,>> I am calculating the RDF from a particular residue to a particular> glycine molecule. I created an index file for both to do this. My> simulation box is 1.5nm, but the RDF values are in the range of 2nm-3nm.> I have viewed my trajectory and all the components stay inside the box.> Please