Thank you! I have missed it somehow. I can still use my xtc trajectory.<br><br>Steven<br><br><div class="gmail_quote">On Wed, May 9, 2012 at 3:16 PM, Javier Cerezo <span dir="ltr">&lt;<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div bgcolor="#FFFFFF" text="#000000">
    The trr file has something wrong. Look at &quot;Coords&quot;, it has 0 frames<br>
    <br>
    You may have forgotten to set nstxout to a non-zero value?<br>
    <br>
    Javier<br>
    <br>
    El 09/05/12 16:10, Steven Neumann escribió:
    <div><div class="h5"><blockquote type="cite">I added one water molecule in my topology to all water
      molecules:<br>
      <br>
      [ molecules ]<br>
      ; Compound        #mols<br>
      Alanine            40<br>
      SOL               724<br>
      <br>
      Maybe I should add aditional line like:<br>
      <br>
      [ molecules ]<br>
      ; Compound        #mols<br>
      Alanine            40<br>
      SOL               723<br>
      SOL                  1<br>
      <br>
      What do you think?<br>
      <br>
      <br>
      <div class="gmail_quote">On Wed, May 9, 2012 at 3:04 PM, Steven
        Neumann <span dir="ltr">&lt;<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>&gt;</span>
        wrote:<br>
        <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Checking
          file md.trr<br>
          trn version: GMX_trn_file (single precision)<br>
          Reading frame       0 time    0.000<br>
          # Atoms  2569<br>
          Last frame       2000 time 100000.000<br>
          <br>
          <br>
          Item        #frames Timestep (ps)<br>
          Step          2001    50<br>
          Time          2001    50<br>
          Lambda        2001    50<br>
          Coords           0<br>
          Velocities    2001    50<br>
          Forces           0<br>
          Box           2001    50<br>
          <br>
          Well, it looks ok. Any suggestions?
          <div>
            <div>
              <br>
              <br>
              <div class="gmail_quote">
                On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo <span dir="ltr">&lt;<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>&gt;</span>
                wrote:<br>
                <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
                  <div bgcolor="#FFFFFF" text="#000000"> Sorry, I saw
                    now the command line you&#39;ve posted. Did you check
                    your trr with gmxcheck?
                    <div><br>
                      <br>
                      El 09/05/12 15:49, Steven Neumann escribió: </div>
                    <blockquote type="cite">hello gmx users,
                      <div>
                        <div><br>
                          <br>
                          I am sorry for bothering you but I was
                          searching mailing list and no results. I have
                          a problem with my test particle insertion as I
                          run the workflow I described previously with
                          my mdp:<br>
                          <br>
                          title       = Test Particle Insertion<br>
                          ; Run parameters<br>
                          integrator  = tpi       <br>
                          nsteps      = 50000000    ; 100 ns<br>
                          dt          = 0.002     ; 2 fs<br>
                          ; Output control<br>
                          nstxout     = 0          ; suppress .trr
                          output ; output coordinates every 25 ps<br>
                          nstvout     = 25000     ; velocities to output
                          every 25000 steps<br>
                          nstenergy   = 1000      ; save energies every
                          2 ps<br>
                          nstlog      = 1000      ; update log file
                          every 2 ps<br>
                          nstxtcout   = 100000         ; suppress
                          (tlumic) xtc trajectory<br>
                          energygrps  = System<br>
                          continuation    = no           ; first
                          dynamics run<br>
                          constraint_algorithm = lincs    ; holonomic
                          constraints <br>
                          constraints     = all-bonds     ; all bonds
                          (even heavy atom-H bonds) constrained<br>
                          lincs_iter      = 1             ; accuracy of
                          LINCS<br>
                          lincs_order     = 4             ; also related
                          to accuracy<br>
                          ; Neighborsearching<br>
                          ns_type     = grid      ; search neighboring
                          grid cells<br>
                          nstlist     = 5         ; 10 fs<br>
                          vdwtype     = Switch<br>
                          rvdw-switch = 1.0<br>
                          rlist       = 1.4       ; short-range
                          neighborlist cutoff (in nm)<br>
                          rcoulomb    = 1.4       ; short-range
                          electrostatic cutoff (in nm)<br>
                          rvdw        = 1.2       ; short-range van der
                          Waals cutoff (in nm)<br>
                          ewald_rtol  = 1e-5      ; relative strenght of
                          the Ewald-shifted potential rcoulomb<br>
                          ; Electrostatics<br>
                          coulombtype     = PME       ; Particle Mesh
                          Ewald for long-range electrostatics<br>
                          pme_order       = 4         ; cubic
                          interpolation<br>
                          fourierspacing  = 0.12      ; grid spacing for
                          FFT<br>
                          ; Temperature coupling is on<br>
                          tcoupl      = V-rescale                     ;
                          modified Berendsen thermostat<br>
                          tc_grps     = System                 ; two
                          coupling groups - more accurate<br>
                          tau_t       = 0.1                            
                          ; time constant, in ps<br>
                          ref_t       = 318                         ;
                          reference temperature, one for each group, in
                          K<br>
                          ; Pressure coupling is on<br>
                          pcoupl      = Parrinello-Rahman             ;
                          pressure coupling is on for NPT<br>
                          pcoupltype  = isotropic                     ;
                          uniform scaling of box vectors<br>
                          tau_p       = 2.0                           ;
                          time constant, in ps<br>
                          ref_p       = 1.0                           ;
                          reference pressure, in bar<br>
                          compressibility = 4.5e-5                    ;
                          isothermal compressibility of water, bar^-1<br>
                          ; Periodic boundary conditions<br>
                          pbc         = xyz       ; 3-D PBC<br>
                          ; Dispersion correction<br>
                          DispCorr    = EnerPres  ; account for cut-off
                          vdW scheme<br>
                          ; Velocity generation<br>
                          gen_vel     = yes       ; assign velocities
                          from Maxwell distribution<br>
                          gen_temp    = 318       ; temperature for
                          Maxwell distribution<br>
                          gen_seed    = -1        ; generate a random
                          seed<br>
                          <br>
                          Then My log file:<br>
                          <br>
                          <br>
                           The temperature for test particle insertion
                          is 318.000 K<br>
                          <br>
                          Started Test Particle Insertion on node 0 Wed
                          May  9 14:18:18 2012<br>
                          <br>
                          Will insert 3 atoms with partial charges<br>
                          <br>
                          Will insert 50000000 times in each frame of
                          md318.trr<br>
                          Will use the same neighborlist for 5
                          insertions in a sphere of radius 0.050000<br>
                          <br>
                            &lt;V&gt;  =         -nan nm^3<br>
                            &lt;mu&gt; =         -nan kJ/mol<br>
                          No MEGA Flopsen this time<br>
                          <br>
                               R E A L   C Y C L E   A N D   T I M E   A
                          C C O U N T I N G<br>
                          <br>
                           Computing:         Nodes     Number    
                          G-Cycles    Seconds     %<br>
                          ------------------------------
                          <div>-----------------------------------------<br>
                             Rest                   4                  
                            5.218        1.9   100.0<br>
-----------------------------------------------------------------------<br>
                             Total                  4                  
                            5.218        1.9   100.0<br>
-----------------------------------------------------------------------<br>
                            <br>
                                Parallel run - timing based on
                            wallclock.<br>
                            <br>
                                           NODE (s)   Real (s)      (%)<br>
                                   Time:      0.485      0.485    100.0<br>
                                           (Mnbf/s)   (MFlops)  
                            (steps/hour)<br>
                            Performance:      0.000     
                            0.000            0.0<br>
                            Finished mdrun on node 0 Wed May  9 14:18:19
                            2012<br>
                            <br>
                            <br>
                            <br>
                            Files are empty. Do you have any clue what
                            is happening?<br>
                            <br>
                            Thank you for your time,<br>
                            <br>
                            Steven
                            <div>
                              <div> <img src=""></div>
                            </div>
                          </div>
                          <br>
                          <br>
                          <div class="gmail_quote">On Wed, May 9, 2012
                            at 1:45 PM, Javier Cerezo <span dir="ltr">&lt;<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>&gt;</span>
                            wrote:<br>
                            <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
                              <div bgcolor="#FFFFFF" text="#000000"> Hi
                                Steven<br>
                                <br>
                                As I remember, TPI is based on the
                                calculation of the potential at every
                                conformation from the already computed
                                simulation (inserting the particle in
                                every snapshot), so velocities are not
                                used.<br>
                                <br>
                                Anyway, use both and see if there are
                                any differences.<br>
                                <br>
                                Javier<br>
                                <br>
                                El 09/05/12 11:27, Steven Neumann
                                escribió:
                                <div>
                                  <div>
                                    <blockquote type="cite">Dear Gmx
                                      Users,<br>
                                      <br>
                                      I am running TPI of the water in
                                      the system containing free amino
                                      acids. Steps:<br>
                                      <br>
                                      1. I run the NPT simulation of 100
                                      ns to equilibrate the system.<br>
                                      2. I added 1 extra water molecule
                                      to the final pdb file (converted
                                      from gro) and to topology<br>
                                      3. I creaded tpi.tpr using grompp
                                      using new pdb file with extra
                                      water molecule<br>
                                      4. mdrun –s tpi298.tpr -rerun
                                      md298.trr -deffnm tpi298 -tpi
                                      tpi298.xvg -tpid tpid298.xvg<br>
                                      <br>
                                      My question: Is it better generate
                                      new velocities in my mdp file
                                      (continuation = yes, gen_vel = no,
                                      tpi integrator) for a pdb file or
                                      use velocities from previous
                                      simulations (gro file)? <br>
                                      If the second option is more
                                      appropriate what velocity shall I
                                      adjust to the extra water
                                      molecule?<br>
                                      <br>
                                      I will appreciate your reply.<br>
                                      <br>
                                      Steven<br>
                                      <br>
                                      <fieldset></fieldset>
                                      <br>
                                    </blockquote>
                                    <br>
                                  </div>
                                </div>
                                <span><font color="#888888">
                                    <div>-- <br>
                                      Javier CEREZO BASTIDA<br>
                                      PhD Student<br>
                                      Physical Chemistry<br>
                                      Universidad de Murcia<br>
                                      Murcia (Spain)<br>
                                      Tel: <a href="tel:%28%2B34%29868887434" value="+34868887434" target="_blank">(+34)868887434</a>
                                    </div>
                                  </font></span></div>
                              <br>
                              --<br>
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                              to the list. Use the<br>
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                            </blockquote>
                          </div>
                          <br>
                          <br>
                          <fieldset></fieldset>
                          <br>
                        </div>
                      </div>
                    </blockquote>
                    <div>
                      <div> <br>
                        <div>-- <br>
                          Javier CEREZO BASTIDA<br>
                          PhD Student<br>
                          Physical Chemistry<br>
                          Universidad de Murcia<br>
                          Murcia (Spain)<br>
                          Tel: <a href="tel:%28%2B34%29868887434" value="+34868887434" target="_blank">(+34)868887434</a>
                        </div>
                      </div>
                    </div>
                  </div>
                  <br>
                  --<br>
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                </blockquote>
              </div>
              <br>
            </div>
          </div>
        </blockquote>
      </div>
      <br>
      <br>
      <fieldset></fieldset>
      <br>
    </blockquote>
    <br>
    <div>-- <br>
      Javier CEREZO BASTIDA<br>
      PhD Student<br>
      Physical Chemistry<br>
      Universidad de Murcia<br>
      Murcia (Spain)<br>
      Tel: <a href="tel:%28%2B34%29868887434" value="+34868887434" target="_blank">(+34)868887434</a>
    </div>
  </div></div></div>

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