[gmx-users] .mtx file
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 23 19:00:49 CEST 2010
Nilesh Dhumal wrote:
> Hello Justin,
>
> I am using Gromacs 4.0.5 version.
> I am getting the same error without specifying -o option.
You could try upgrading to 4.0.7, but I don't know if there have been any
changes in the code that would affect this behavior. Otherwise, submit a bugzilla.
-Justin
>
> 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
>>>>>> posting! Please don't post (un)subscribe requests to the list. Use
>>>>>> the www interface or send it to gmx-users-request at gromacs.org.
>>>>>> Can't
>>>>>> 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
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting! Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org. Can't
>>>> 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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org. Can't 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
========================================
More information about the gromacs.org_gmx-users
mailing list