Hi Justin<br><br>Below is my nvt.mdp (nvt equilibration) file.i think probably you can have look at it and its not such big.<br><br>define          =                 -DFLEXIBLE    <br>integrator     =                  md        <br>
nsteps         =                  50000       <br>dt                =                  0.002      <br>nstxout        =                  100       <br>nstvout        =                  100       <br>nstenergy    =                  100       <br>
nstlog         =                  100        <br>constraint_algorithm     = shake    <br>constraints        =            none    <br>unconstrained_start    =    yes   <br>shake_tol        =              0.0001 <br>morse            =               no     <br>
ns_type        =                grid        <br>nstlist        =                   5        <br>rlist        =                      1.0       <br>coulombtype    =            PME        <br>rcoulomb    =                  1.0        <br>
vdwtype        =               Cut-off       <br>rvdw        =                    1.0        <br>pme_order    =                4       <br>fourierspacing    =          0.16        <br>pbc        =                     xyz        <br>
tcoupl        =                 V-rescale    <br>tc-grps        =                system    <br>tau_t        =                   0.1        <br>ref_t        =                   300        <br>DispCorr    =                 Ener   <br>
gen_vel        =              yes        <br>gen_temp    =               300       <br>gen_seed    =               173529    <br><br>regarding the plot i too know that one should use Xmgrace to plot. In the pressure Vs time(lysozyme tutorial) you have got two graphs. i to got the pressure Vs time (black line graph) my question is how to get the running average ( red line) and plot?. does i need any command to get the running average?. any help is highly appreciated.<br>
<br>Regards<br>Vinoth<br><br><div class="gmail_quote">On Thu, Oct 21, 2010 at 4:56 PM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
vinothkumar mohanakrishnan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi justin<br>
<br>
I found what went wrong and i corrected my mdp file.now the system equilibrated to the desired temperature 300 K (plus r minus 30 K) is this ok?<br>
</blockquote>
<br></div>
This is impossible to assess without seeing your .mdp settings.  A fluctuation of 10% is probably fine.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Apart from that i want to know how you plot the average running pressure and density in your tutorial for lyzosyme (redline). i just  want to do that for DCE. any help is highly appreciated.<br>
<br>
</blockquote>
<br></div>
Xmgrace.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Regards<br>
Vinoth<div class="im"><br>
<br>
On Wed, Oct 20, 2010 at 5:33 PM, Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt; wrote:<br>

<br>
<br>
<br>
    vinothkumar mohanakrishnan wrote:<br>
<br></div><div class="im">
        Hi Justin<br>
<br>
        I corrected the mistake what you said and i am able to run<br>
        energy minimisation and equilibration. but when i view my em.gro<br>
        and equilibration.gro in VMD it seems to me that the bonds<br>
        between the atoms are broken in molecules.I used g_energy to<br>
        check weather the system has<br>
<br>
<br>
    VMD tries to guess where bonds should be, but does not always do a<br>
    good job. Your topology defines bonds.  These are the only bonds<br>
    that there will be.  None can be broken or formed in standard MD.<br>
<br>
<br>
        equilibrated to the required temperature (300K) i found that the<br>
        variation in the temperature was 100K (plus r minus) . i am not<br>
        able find out what went wrong. any help is highly appreciated.<br>
<br>
<br>
    Without seeing your .mdp file, there&#39;s no way to know.  The<br>
    fluctuation does seem too high, though, unless your system really is<br>
    just that unstable.  Are other properties converged - potential<br>
    energy, density, etc?  What type of ensemble are you using?<br>
<br>
    -Justin<br>
<br>
        Regards<br>
        Vinoth<br>
<br>
<br>
        On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul<br>
        &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br></div><div><div></div><div class="h5">
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
           vinothkumar mohanakrishnan wrote:<br>
<br>
               Dear Justin<br>
<br>
               what corrections i should make to ffoplsaan.itp to make it<br>
               correct. what i should give instead of CAB and CLAA?.<br>
<br>
<br>
           You must use atom types, not names.  Unfortunately, you&#39;ve<br>
        chosen to<br>
           use atom names, which are also types, which makes all of this<br>
        quite<br>
           confusing if you&#39;re not sure what you&#39;re doing.<br>
<br>
           You defined two new atom types - opls_966 (CAB) and opls_967<br>
        (CLAA),<br>
           which are the only indicators you are allowed to use if<br>
        introducing<br>
           new types.  Thus, references to atom names (CAC, CLAD) will<br>
        generate<br>
           fatal errors.<br>
<br>
<br>
               i copied the .rtp .atp .itp files from<br>
               usr/local/gromacs/share/gromacs/top to my working<br>
        directory and<br>
               added these parameters to the corresponding files. what<br>
        you mean<br>
               is should i need to add these parameters to the source<br>
        directory<br>
               ( usr/local/gromacs/share/gromacs/top)?<br>
<br>
<br>
           Your topology needs to be consistent with whatever files need<br>
        to be<br>
           included. By default, Gromacs checks the working directory first,<br>
           but if you&#39;ve moved to a new (sub)directory to carry out further<br>
           steps, the grompp will not find your modified files, but will<br>
           instead locate only the default force field files in $GMXLIB.<br>
            Either keep all your work in one directory (which can get<br>
        messy),<br>
           or make use of the &quot;include&quot; keyword in the .mdp file.  Any<br>
           directory specified there will be searched after the working<br>
           directory, but before $GMXLIB.<br>
<br>
           -Justin<br>
<br>
               Regards<br>
               Vinoth<br>
<br>
<br>
               On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul<br>
               &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;<br>
               &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
                  vinothkumar mohanakrishnan wrote:<br>
<br>
                      Hi all<br>
<br>
                      i added new atomtype for dichloroethane (DCE) and<br>
        added the<br>
                      corresponding parameters in the .rtp, .atp,<br>
        .bon.itp, .nb.itp<br>
                      respectively. given below are my additions to the<br>
               corresponding<br>
                      files respectively.<br>
<br>
                      *ffoplsaa.rtp*<br>
<br>
                      [ DCE ]<br>
                       [ atoms ]<br>
                       CLAA opls_967 -0.2270  1<br>
                       CAB  opls_966  0.2270  1<br>
                       CAC  opls_966  0.2270  2<br>
                       CLAD opls_967 -0.2270  2<br>
<br>
                      [ bonds ]<br>
                       CLAA    CAB<br>
                       CAB    CAC<br>
                       CAC    CLAD<br>
<br>
                      [ angles ]<br>
                       CLAA    CAB    CAC<br>
                       CAB    CAC    CLAD<br>
<br>
                      [ dihedrals ]<br>
                       CLAA    CAB    CAC    CLAD<br>
<br>
                      *ffoplsaa.atp*<br>
<br>
                       opls_966   14.02700  ; CH2 for DCE<br>
                       opls_967   35.45300  ; CL for DCE<br>
<br>
                      *ffoplsaabon.itp*<br>
<br>
                      [bondtypes]<br>
                      CLAA  CAB     1    0.17870   194137.6   ; CL-CH2<br>
        for DCE<br>
                      CAB   CAC     1    0.15300   259408.0   ; CH2-CH2<br>
        for DCE<br>
                      CAC   CLAD    1    0.17870   194137.6   ; CL-CH2<br>
        for DCE<br>
<br>
                      [angletypes]<br>
                      CLAA  CAB   CAC       1   108.200    368.192   ;<br>
        C-C-CL<br>
               for DCE<br>
                      CAB   CAC   CLAD      1   108.200    368.192   ;<br>
        C-C-CL<br>
               for DCE<br>
<br>
                      [dihedraltypes]<br>
                      CLAA   CAB     CAC   CLAD     3     20.76096<br>
         -0.4184                 27.011904  0.00000   0.00000   0.00000<br>
        ; for DCE<br>
<br>
<br>
                  You shouldn&#39;t be using atom names in the [*types]<br>
        directives.<br>
                What<br>
                  you should be using are the interpolated types from<br>
               ffoplsaanb.itp,<br>
                  thus you have only utilized opls_966 (CAB) and<br>
        opls_967 (CLAA).<br>
<br>
                      *ffoplsaanb.itp*<br>
<br>
<br>
                      opls_966   CAB    6    14.02700    0.227       A                  3.98000e-01<br>
                       4.76976e-01 ; CH2 of DCE<br>
                      opls_967   CLAA   17   35.45300   -0.227       A                  3.16000e-01<br>
                       0.20920e+01 ; Cl of DCE<br>
<br>
                      *dce.pdb*<br>
<br>
                      HETATM    1 CLAA DCE     1       6.300  -2.280          1.360  1.00<br>
                      20.00            CL<br>
                      HETATM    2  CAB DCE     1       5.060  -3.540          1.500  1.00<br>
                      20.00             C<br>
                      HETATM    3  CAC DCE     1       4.320  -3.740          0.170  1.00<br>
                      20.00             C<br>
                      HETATM    4 CLAD DCE     1       3.270  -2.350<br>
         -0.210  1.00<br>
                      20.00            CL<br>
<br>
                      After adding all this, when i run grompp i get the<br>
        error as<br>
                      *fatal error Unknown bond_atomtype CLAA*. can any<br>
        one tell me<br>
                      why this happens?.<br>
<br>
<br>
                  Have you been sure to #include the correct (modified)<br>
        force field<br>
                  files?  That is, if you made a local copy and adjusted<br>
        them,<br>
               these<br>
                  won&#39;t be the files that pdb2gmx will #include by default.<br>
<br>
                  -Justin<br>
<br>
                      Regards<br>
                      Vinoth<br>
<br>
<br>
                  --     ========================================<br>
<br>
                  Justin A. Lemkul<br>
                  Ph.D. Candidate<br>
                  ICTAS Doctoral Scholar<br>
                  MILES-IGERT Trainee<br>
                  Department of Biochemistry<br>
                  Virginia Tech<br>
                  Blacksburg, VA<br>
                  jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt;<br>
        &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540)<br>
<br>
               231-9080<br>
<br>
                  <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br>
<br>
           --     ========================================<br>
<br>
           Justin A. Lemkul<br>
           Ph.D. Candidate<br>
           ICTAS Doctoral Scholar<br>
           MILES-IGERT Trainee<br>
           Department of Biochemistry<br>
           Virginia Tech<br>
           Blacksburg, VA<br>
           jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540)<br>
        231-9080<br>
           <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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    Justin A. Lemkul<br>
    Ph.D. Candidate<br>
    ICTAS Doctoral Scholar<br>
    MILES-IGERT Trainee<br>
    Department of Biochemistry<br>
    Virginia Tech<br>
    Blacksburg, VA<br>
    jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540) 231-9080<br>
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</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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