[gmx-users] Fwd: Fwd: Need some assistence

[Ruben Cloete]

Could someone assist me seeing as i am only a beginner at molecular dynamics

i have generated models using modeller software and selected the best 
model based on DOPE GA341 and

Prosa now i have performed energy minimisations using gromacs software.

I further energy refined the structures using gromacs.

The steps were as follows: For in vacuo minimisation

Steepest descent 1000 steps and conjugated gradient of 3000 steps.

Could you perhaps just check the parameter files  (st.mdp and con.mdp)
and commands (commands) used to ensure the correct procedures and
selections were made in order to ensure my peace of mind. The command
files contain outputs

I also performed minimisations using periodic boundary conditions adding
ions and solvated the system

this also were performed using similar conditions as in the in vacuo
minimisation.

These files are also attached parameter files (em.mdp and con1.mdp) and
commands (commands1).

Thank you very much i appreciate any and all advice given by you.

Best Regards

Ruben Cloete
South Africa





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