[gmx-users] energy minimization runs with error like too large force on atom 7773

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 22 09:21:32 CET 2004

On Sun, 2004-11-21 at 17:32 -0800, HR Hu wrote:
> Hi, dear all,
> I am new in gromacs. Recently I perform a MD experiment with
> Gromacs3.2.1. I do agree that this software is so powerful.
> Here is my question: when I process to mdrun with em.mdp, the em.log
> output file shows the following information.
> "Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> Steepest Descents converged to machine precision in 960 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy = -4.9661972e+05
> Maximum force = 5.3885300e+05 on atom 7773
> Norm of force = 3.2573675e+06
> I try increase the stepsize "emstep" from 0.01 to 0.1, it still don't
> converge, the error remains. Then I check the atom 7773 and foud that
> it is an oxygen in a SOL water. Furthermore it is the bulk one, not
> the crystallographic one I keep in my system. As I know, the SPC216
> model is quite well optimized. Also I try to ignore this to process
> further position-restrained MD. It fails. I don't know why?

The energy is too low, you probably have a water molecule that has a
hydrogen too close to a negative charge in your protein.

> Second question is that how to discriminate the crystallographic water
> and the solvation ones generated by genbox? In original protein PDB
> files, the crystall ones are marked as HOH, but thereafter they are
> marked as same as the solvation water with SOL. I guess the atom
> sequense don't change before and after adding solvation water, am I
> right?
That's right. You will have your crystal waters first. They will
exchange quite soon though.
> My third, also the last one is that about my system contains protein,
> ligand and crystallographic water. If I attach the PRODRG converted
> ligand.pdb directly at the end of pdb/gro file(protein and HOH's atom
> No. or residue No. are continuous) generated by pdb2gmx. It will be
> error when process to genion. So I have to insert the ligand between
> the protein and HOH manuually to keep the No. of HOH and SOL
> continuous. Is there any other way to solve this negligible problem
> since it is too difficult for me to change the atom number and HOH
> numbere one by one if there are many crystallographic waters.
yes, write in your top at the end:

protein 1
sol X
ligand 1
sol Y

> Thanks in advance!
> Hairong Hu
> Ph.D.candidate
> Depart. of Chemistry
> Fudan University
> Shanghai, 200433,
> China
> hrhu75 at 163.com
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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