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
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,
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
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*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