[gmx-users] .mtx file

[Nilesh Dhumal]

Hello,
I am trying to calculate the normal mode analysis for ionic liquids.
I could do energy minimzation. I could not get .mtx file for further
analysis to get normal modes.

THis is my energy minimization file

define                   = -DFLEXIBLE

constraints              = none

integrator               = L-bfgs

tinit                    = 0

nsteps                   = 15000

nbfgscorr                = 50

emtol                    = .001

emstep                   = 0.1

gen_vel                  = yes

gen-temp                 = 300

nstcomm                  =  1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency

nstlist                  = 0

; ns algorithm (simple or grid)

ns-type                  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc                      = no

; nblist cut-off

rlist                    = 0

domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics
coulombtype              = Cut-Off

rcoulomb-switch          = 0

rcoulomb                 = 0

; Dielectric constant (DC) for cut-off or DC of reaction field

epsilon-r                = 1

; Method for doing Van der Waals

vdw-type                 = Cut-off

; cut-off lengths

rvdw-switch              = 0

rvdw                     = 0


grompp -f minim.mdp -t 1.trr -c test.pdb -o 1.tpr -zero -p test.top

 mdrun -v -s 1.tpr -deffnm new_nm -mtx new_nm.mtx

I could not get the new_nm.mtx file.
Can you tell me where I am going wrong.

THanks

Nilesh