[gmx-users] .mtx file

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 22 23:07:31 CEST 2010 


Nilesh Dhumal wrote:
> Hello Justin
> 
> In manual (Manual-4.0) and  g_nmens -h (help), the extension of output
> file is .xtc. If I use the default output file name still I am getting the
> same error.
> 

I know what the help information says, I was just trying to clarify if what you 
had shown was actually a direct copy-and-paste from a terminal or something else 
processed through your memory.  Whether or not you were specifying the same 
output name as default (or thought you were) is irrelevant, I was just 
suggesting a test - don't specify anything at all for the -o flag, just in case 
you made some sort of typo.  If you get the same error when you are not 
specifying anything at all with -o, then at least post the Gromacs version 
you're using (which I asked for before) to see if any of the developers has an 
idea about what could be going on.  If the default output is giving a fatal 
error, something is probably wrong in the code.

-Justin

> Nilesh
> 
> On Thu, April 22, 2010 4:01 pm, Justin A. Lemkul wrote:
> 
>> 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
>>
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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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

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

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