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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 28 12:41:35 CEST 2011

On 4/28/2011 6:10 PM, Ruben Cloete wrote:
> 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.

Seems fine - but you should look up in section 7.3 of the manual what 
everything does and satisfy yourself that your choices make sense with 
what you know about molecular simulations. Read the relevant sections 
earlier in the manual and do all the tutorial material and textbook 
reading you can find, even if it's off-topic for you.


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