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

[HR Hu]

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?

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?

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.

Thanks in advance!

Hairong Hu
Ph.D.candidate
Depart. of Chemistry
Fudan University
Shanghai, 200433,
China
hrhu75 at 163.com