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. 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 > > > -- 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
