[gmx-users] .mtx file

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> 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.

Did the above g_nmens command come directly from a copy-paste from your 
terminal?  Looking into the code, I see no way that writing an .xtc file would 
be misinterpreted as writing a binary topology, thus giving that error.  Check 
for typos, specifically in the file extension.  If you're using the default 
output file name, you don't even have to specify it.

If it still doesn't work, report back.  It might also be useful to know your 
Gromacs version in case of problems.

-Justin

> 
> 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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>>
> 
> 
> 

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

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

========================================