[gmx-users] .mtx file

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> 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
> 

Be careful about setting -zero.  If you're trying to get past error messages, 
that usually means you have missing parameters and could end up with nonsense as 
a result.

>  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.
> 

You aren't getting the .mtx file because you're telling mdrun to do energy 
minimization, not normal modes.  L-BFGS is an EM method.  Set "integrator = nm" 
to do normal modes.

-Justin

> THanks
> 
> Nilesh
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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