[gmx-users] Related to energy minimization

ISHRAT JAHAN jishrat17 at gmail.com
Mon Sep 10 11:43:57 CEST 2018

Dear all,
I am trying to do energy minimization of two docked protein. At the energy
minimization step during MD simulation process, the em.gro file is found to
be broken due to which equilibration of protein does not occur and core
dumped error has been found.
Please help me in this regard. I am attaching my em.mdp file and snapshot
of em.gro 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 kJ/mol
nsteps          = 2000          ; Maximum number of (minimization) steps to
nstenergy       = 1             ; Write energies to disk every nstenergy
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         = grid  ; Method to determine neighbor list (simple, grid)
coulombtype = PME               ; Longrange electrostatics (Ewald)
rvdw = 1.0
rlist = 1.0
rcoulomb = 1.0
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
constraints     = none          ; Bond types to replace by constraints
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
[image: Screenshot_from_2018-09-10_14_59_11.jpg]

Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh

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