[gmx-users] .mtx file

Nilesh Dhumal ndhumal at andrew.cmu.edu
Fri Apr 23 18:27:19 CEST 2010 

Hello Justin,

I am using Gromacs 4.0.5 version.
I am getting the same error without specifying -o option.

Nilesh



On Thu, April 22, 2010 5:07 pm, Justin A. Lemkul wrote:
>

>
> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ========================================
>>>>> --
>>>>> 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
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>>>>> post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>> --
>>> ========================================
>>>
>>>
>>>
>>> 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
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>>> Please search the archive at http://www.gromacs.org/search before
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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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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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