[gmx-users] The energy minimization....
t.piggot at bristol.ac.uk
Fri Aug 17 15:47:11 CEST 2007
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.
--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
> 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=
> 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
> 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!
>> 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.
t.piggot at bristol.ac.uk
University of Bristol, UK.
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