Tsjerk Wassenaar wrote:
1. First i give the sequence an in vaccuo steepest descent run
(emtol=1000 in mdp file)
2. then i give the sequence an in vaccuo conjugate gradient run
(emtol = 100, then 50, 10, 5 and 2 in the mdp file)
3. next i give it an md step in vaccum with temp & pressure coupling on.
Now spend a brief moment thinking what would happen if you have a
molecule in vacuum and you say you want to simulate it at constant
pressure (i.e. turn the pressure coupling on).
4. I view the trajectory and if i find the rmsd quite less then i
proceed to adiing the box, else i repeat the md in vaccuo step by
increasing the time.
Energy minimization is not about RMSD.., did you consider checking the
energy? Think of the reasons to perform energy minimization and, as an
excercise, think of the energy terms you should be particularly
interested in.
Agreed. I retract my earlier comment about "reasonableness"! Sometimes
you get what you pay for on this list!
5. Now i add the box and then water. Next i give it a position
Restraint run and then the md run.
Is this the right method?
Also, as my sequence contains peptoid residues (sidechains are
appended to the amide nitrogen rather then alpha carbon) i am unable
to calculate the dihedral angles. How to proceed?
Don't. Don't even think of going there, without understanding
molecular simulations of 'ordinary' biological systems, both in terms
of theory and practice. Besides that, simulations of non-standard
systems require even more knowledge, for instance regarding the
determination of parameters.
Agreed. As I seem to say weekly on here, learn to walk before trying to run.
Mark
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