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On 4/28/2011 6:10 PM, Ruben Cloete wrote:
<blockquote cite="mid:4DB920E7.4060608@sanbi.ac.za" type="cite">
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Could someone assist me seeing as i am only a beginner at
molecular dynamics<br>
<br>
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<big><big>i have generated models using </big></big>modeller
software and selected the best model based on DOPE GA341 and <br>
<pre><big><big>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.</big></big>
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<br>
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.<br>
<br>
Mark<br>
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