[gmx-users] The energy minimization....

[Mark Abraham]

MoJie Duan wrote:
>  >So look at your structures like I said last time! I'm not here to give
>  >my valuable time giving free advice in order to have it ignored...
> 
> Thank you very much for your kindness and patience. Maybe sometimes my 
> questions seems to be silly and boring, my knowledge about GROMACS is 
> really lack, sorry.....
> 
> Actually, I really cannot understand what you said yesterday. Did you 
> mean is there any difference between the atom coordinates of ATP before- 
> and after- minimization?


There would normally be some differences visible. If your topology was
badly broken, then you would usually see where it was broken.

>  I found there are not any difference between 
> these two structure.
> (There are also not any obvious collision between atoms of ATP when 
> represent it by Rasmol)

OK, so that means your structure is in a flat area of the potential
surface defined by your topology. If the topology is sound, then you're
in business.

>  > >mjduan at smail.hust.edu.cn wrote:
>  >
>  > >To reply to a list email, just reply as you would to any other email.
>  >
>  >
>  > >The .top succeeded in minimizing the solvated structure, so that's a
>  > >good start. I think I can see that I was being too subtle for you
>  > >earlier with my suggestion that you think about observables that would
>  > >tell you whether your topology was working. Have you looked at the
>  > >before- and after-minimization structures to see whether they make
>  > >sense according to your training at recognizing chemical structures
>  > >that will be energy minima? If all of your components look 
> reasonable post-minimization on their own,
>   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^what means?

My first recommendation was to minimize and/or equilibrate these
structures on their own, and now I suggest doing them also in solvent.
This will help you eliminate sources of problems and guide you to what
the real problem is. Divide and conquer...

>  > > and there were no significant warnings
>  > >or errors from grompp then your topolog ies probably are OK too.
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^just like I said in last email, there 
> are not any warnning and error from grompp.

That's fine, then.

>  > >Thenyou should go back and approach your original problem of getting
>  > >working topology f or your combination system.
>                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^I cannot run the 
> full MD SImulation for ATP individually, so I think maybe there are 
> something problem with it (I used the same minim.mdp can successfully do 
> the energy minimization of the protein individually).  I really confused.

OK, so here's your problem. Work out what's breaking and why. Read the
error messages and look at the structures. Understand what each of your
.mdp file options does.

Mark