[gmx-users] problem in energy minimization of the inflted system

Parul tew parultew at gmail.com
Mon Mar 28 06:50:11 CEST 2011

Dear GMX users,
 I am facing problem while doing energy minimization of the inflated system
of a protein with membrane. I inflated the system and updated the removed
lipids in the topology file. Now I am stuck during the energy minimization
state. Below is the .mdp file for minimization.


; minim_1.mdp - used as input into grompp to generate em_1.tpr

integrator  = cg        ; Algorithm (cg = conjugate gradient minimization)

emtol       = 1000.0    ; Stop minimization when the maximum force < 1000.0

emstep      = 0.01      ; Energy step size

nsteps      = 50000     ; Maximum number of (minimization) steps to perform

nstlist     = 1         ; Frequency to update the neighbor list and long
range forces

ns_type     = grid      ; Method to determine neighbor list (simple, grid)

rlist       = 1.2       ; Cut-off for making neighbor list (short range

coulombtype = PME       ; Treatment of long range electrostatic interactions

rcoulomb    = 1.2       ; Short-range electrostatic cut-off

rvdw        = 1.2       ; Short-range Van der Waals cut-off

gen_vel     = yes

define      = DSTRONG_POSRES

when I run this using the command

*grompp –f minim_1.mdp –c system_inflated.gro topol.top –o em_1.tpr *

it generates the em_1.tpr file but does not generate any md_out.mdp  file
and it gives the following 2 notes

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#

checking input for internal consistency...

processing topology...

*NOTE 1 [file topol.top, line 24414]:*


  System has non-zero total charge: 1.400002e+01

  processing coordinates...

double-checking input for internal consistency...

Reading position restraint coords from system_inflated.gro

renumbering atomtypes...

converting bonded parameters...

initialising group options...

processing index file...

Analysing residue names:

Opening library file /usr/local/Gromacs/share/top/aminoacids.dat

There are:   121      OTHER residues

There are:   408    PROTEIN residues

There are:     0        DNA residues

Analysing Protein...

Analysing Other...

Making dummy/rest group for T-Coupling containing 9931 elements

Making dummy/rest group for Acceleration containing 9931 elements

Making dummy/rest group for Freeze containing 9931 elements

Making dummy/rest group for Energy Mon. containing 9931 elements

Making dummy/rest group for VCM containing 9931 elements

Number of degrees of freedom in T-Coupling group rest is 29790.00

Making dummy/rest group for User1 containing 9931 elements

Making dummy/rest group for User2 containing 9931 elements

Making dummy/rest group for XTC containing 9931 elements

Making dummy/rest group for Or. Res. Fit containing 9931 elements

Making dummy/rest group for QMMM containing 9931 elements

Checking consistency between energy and charge groups...

Calculating fourier grid dimensions for X Y Z

Using a fourier grid of 216x216x55, spacing 0.119 0.119 0.120

Estimate for the relative computational load of the PME mesh part: 0.96

*NOTE 2 [file aminoacids.dat, line 1]:*


  The optimal PME mesh load for parallel simulations is below 0.5

  and for highly parallel simulations between 0.25 and 0.33,

  for higher performance, increase the cut-off and the PME grid spacing

This run will generate roughly 116 Mb of data

writing run input file...

There were 2 notes

gcq#22: "I Had So Many Problem, and Then I Got Me a Walkman" (F. Black)

understand the note 1 as I haven’t added the ions yet, so the system has

But I am confused about note 2, what changes can I make to .mdp file for the
minimization to run smoothly.


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