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

[TJ Piggot]

Hi you need to explain in detail what steps you are doing before the 
minimisation and also what parameters you are using in your .mdp file 
because i have just run a minimisation of ATP (in water) to test the 
topology in the GROMOS96 ff and it works fine for me, so there must be a 
problem in one of your setup steps or your simulation parameters.

Tom

--On Friday, August 17, 2007 18:15:40 +0800 MoJie Duan 
<mjduan at smail.hust.edu.cn> wrote:

> Hi, Mark:
> I have done the energy minimization and simulation of ATP in vacuum
> individual ( Maybe you have suggested me to do this yesterday, but
> actually I did not understand it, and just do this in solution).
> There are following problems:
> 1. in the energy minimization, the potential energy is positive and in
> 14th step, it's potential energy is "nan". But the ".gro" outfile of
> "mdrun" is just the same as the original file (i.e. the .gro file before
> minimization), the return messages of mdrun is (there are not any
> warning):
>
> ------------------------------
> Getting Loaded...
> Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision)
> Loaded with Money
>
>
> Back Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1#
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+00
>    Number of steps    =     & #160;    200
> Step=    0, Dmax= 1.0e-02 nm, Epot=  1.06678e+05 Fmax= 3.63368e+06, atom=
> 26
> Step=   14, Dmax= 1.2e-06 nm, Epot=          nan Fmax= 3.63313e+06,
>                              ^^^^^^^^^^^^^^^^^^^^^^^
> atom= 26
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1
>
> Double precision normally gives you higher accuracy.
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1#
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1.
> Potential Energy  =  1.0667836e+05
> Maximum for ce     =  3.6336775e+06 on atom 26
> Norm of force     =            nan
> ___________________________________________
>
> 2. in the full MD simulation, the "warning" coming, the messages is:
>
> --------------------------------------------
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.881911 (between atoms 27 and 28) rms nan
> bonds that rotated more than 30 degrees:
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>  atom 1 atom 2  angle  previous, current, constraint length
>      27     28   90.0    0.1610   0.3030      0.1610
> Wrote pdb files with previous and current coordinates
> step 2490, remaining runtime:     0 s   & #160;           Writing final
> coordinates.
>
> Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1#
> step 2500, remaining runtime:     0 s              
> __________________________________________________
>
> And in the ".gro" file after this step, the coordinates of all atoms are
> "nan". So it means there are crash in the structure? Is the crash between
> the atom 27 and 28? How to modify the structure file make it normal?
> Thank you very much!
>
> Duan
>
>
>> MoJie Duan wrote:
>> > > So look at your structures like I said last time! I'm not her e 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.
>
>> 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...
>
>> That's fine, then.
>
>> 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
>
>



----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.