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