[gmx-users] Re: please guide me

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 15 12:55:26 CET 2006

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.


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