[gmx-users] Error energy minimization on protein with implicit water

aiswarya pawar aiswarya.pawar at gmail.com
Thu Feb 9 14:01:38 CET 2012

Dear Gromacs users,

I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps followed are-

pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr

The minim.mdp file =

; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title        = Energy Minimization    ; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp        = /lib/cpp    ; Preprocessor

; Define can be used to control processes
define          = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator    = steep        ; Algorithm (steep = steepest descent
emtol        = 1000.0    ; Stop minimization when the maximum force < 1.0
nsteps        = 5000        ; Maximum number of (minimization) steps to
nstenergy    = 1        ; Write energies to disk every nstenergy steps
energygrps    = System    ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type        = simple      ; Method to determine neighbor list (simple,
coulombtype    = cut-off      ; Treatment of long range electrostatic
rcoulomb    = 1.0        ; long range electrostatic cut-off
rvdw        = 1.0        ; long range Van der Waals cut-off
constraints    = none        ; Bond types to replace by constraints
pbc        = no        ; Periodic Boundary Conditions (yes/no)

I get a note as =
System has non-zero total charge: -4.999996e+00

then i tried using genion step as=

genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log

then again the grompp step and mdrun .
but while doing mdrun i get an error as=

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

but here i have given nsteps as 5000 so why does it stop.
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science

Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
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