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
<[EMAIL PROTECTED]> 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
[EMAIL PROTECTED]
University of Bristol, UK.
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