[gmx-users] [Fwd: question about em in gromacs]

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 19 10:08:44 CET 2004

-------- Forwarded Message --------
From: hrhu75 <hrhu75 at 163.com>
To: spoel at gromacs.org
Cc: spoel at xray.bmc.uu.se
Subject: question about em in gromacs
Date: Fri, 19 Nov 2004 09:54:54 +0800 (CST)
Hi, dear Dr. David,
How are you? 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

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
Depart. of Chemistry
Fudan University
Shanghai, 200433,
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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