[gmx-users] .mtx file

[Nilesh Dhumal]

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.

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
>
>
> ========================================
> --
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