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@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-requ...@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@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-requ...@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@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-requ...@gromacs.org. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? 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