[gmx-users] .mtx file

[Nilesh Dhumal]

Hello Justin,
I could genrate the .mtx file. I followed following steps.

 g_nmeig -f test.mtx -s 1.tpr -of eigenfreq.xvg -v test1.trr

 g_nmtraj -s 1.tpr -v test1.trr -o test.xtc

 g_anaeig -v test1.trr -f test.xtc -s 1.tpr -eig eigenval.xvg

and

g_nmens -v test1.trr -e eigenval.xvg -n test.ndx -s 1.tpr -o ensemble.xtc

For last analysis (g_nmens) I get following error.

Fatal error:Sorry, write_trxframe_indexed can not write tpa

Can you help me resolve this error.

NIlesh


On Thu, April 22, 2010 12:55 pm, Justin A. Lemkul wrote:
>

>
> 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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