md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
help_text='scaling of the friction coefficients (Langevin)')
md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
- md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
+ md_mdpdb = forms.BooleanField(required=True,label='trajectory as PDB')
boxx = forms.FloatField(label='Box X',initial=1000.0,
help_text='box x dimension')
{% if task.md_pdbref %}
<li class="list-group-item task-item">
- <div class="col-md-2"> RMSD </div>
+ <div class="col-md-2"> C<sup>α</sup> RMSD </div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
width="500"> </div>
{% if task.md_pdbref %}
<li class="list-group-item task-item">
- <div class="col-md-2"> Average RMSD vs. temperature </div>
+ <div class="col-md-2"> Average C<sup>α</sup> RMSD vs. temperature </div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
width="500"> </div>
</li>
<li class="list-group-item task-item">
- <div class="col-md-2"> potential energy vs. RMSD</div>
+ <div class="col-md-2"> potential energy vs.
+ C<sup>α</sup> RMSD</div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
width="500"> </div>
</li>
<li class="list-group-item task-item">
- <div class="col-md-2"> RMSD vs. step*replica
+ <div class="col-md-2"> C<sup>α</sup> RMSD vs. step*replica
colored by bath temperature</div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"
{% if task.md_pdbref %}
<li class="list-group-item task-item">
- <div class="col-md-2"> RMSD </div>
+ <div class="col-md-2"> C<sup>α</sup> RMSD </div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
width="500"> </div>
{% if task.md_pdbref %}
<li class="list-group-item task-item">
- <div class="col-md-2"> Average RMSD vs. temperature </div>
+ <div class="col-md-2"> Average C<sup>α</sup> RMSD vs. temperature </div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
width="500"> </div>
</li>
<li class="list-group-item task-item">
- <div class="col-md-2"> potential energy vs. RMSD</div>
+ <div class="col-md-2"> potential energy vs.
+ C<sup>α</sup> RMSD</div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
width="500"> </div>
</li>
<li class="list-group-item task-item">
- <div class="col-md-2"> RMSD vs. step*replica
+ <div class="col-md-2"> C<sup>α</sup> RMSD vs. step*replica
colored by bath temperature</div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"
<li>
PDB files can be downloaded from the PDB database based on given PDB code.
To select only a single chain use PDB_code:chain_id notation (for example
-5G3Q:B), chain_id is case sensitive.
+5G3Q:B), chain_id is case sensitive. For the PDB files containing multiple
+models, only the first models is taken.
<li>
Unres server requires input PDB files with continuous (without breaks)
protein chains. PDB files with gaps in the structure have to be first prepared
Secondary structure restraints can be added to MD and MREMD
simulation in advanced mode. Sequence of letters H,E and C or - for each
residue is used to input helical, extended and no restraints, respectively.
+<li>
+For MD simulations by default the snapshots are written in PDB format to be
+displayed by NGLViewer. In advanced mode, the user can request the compressed
+cx format, which is recommended for larger jobs. In this case, the movie
+in mp4 and ogv formats are rendered and displayed. The movie files can also
+be downloaded for further use.
</ol>
{% endblock %}
<LI><A NAME="tex2html36"
HREF="outputs.html#SECTION00041000000000000000">Summary of the files</A>
<LI><A NAME="tex2html37"
- HREF="outputs.html#SECTION00042000000000000000">The structure of the main output file (out)</A>
+ HREF="outputs.html#SECTION00042000000000000000">The structure of the main output file</A>
<LI><A NAME="tex2html38"
HREF="outputs.html#SECTION00043000000000000000">The thermodynamic quantity and ensemble average (thermal) files</A>
<LI><A NAME="tex2html39"
HREF="outputs.html#SECTION00044000000000000000">The conformation summary with classification (stat) files</A>
-<LI><A NAME="tex2html40"
+<!--<LI><A NAME="tex2html40"
HREF="outputs.html#SECTION00045000000000000000">The histogram files</A>
<LI><A NAME="tex2html41"
- HREF="outputs.html#SECTION00046000000000000000">The rmsd-radius of gyration potential of mean force files</A>
+ HREF="outputs.html#SECTION00046000000000000000">The rmsd-radius of gyration potential of mean force files</A> -->
<LI><A NAME="tex2html42"
HREF="outputs.html#SECTION00047000000000000000">The PDB files</A>
<LI><A NAME="tex2html43"
<P>
These files are written in PDB standard (see. e.g.,
-ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf<FONT COLOR="#0000ff">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</FONT>). The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
+<a href="ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</a>). The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
The Cα
(marked CA) and SC (marked CB) coordinates are output. The CONECT
records specify the Cα - Cα and Cα - SC virtual bonds. Secondary
<DT></DT>
<DD>file.cx - the compressed UNRES coordinate file with information to compute the probability of a given conformation at any temperature.
+<!--
<P>
</DD>
<DT></DT>
<DT></DT>
<DD>file.rmsrgy, file_par_yy.rmsrgy, file_slice_xx.rmsrgy or file_par_yy_slice_xx.rmsrgy - the 2D histogram(s) of rmsd from the experimental structure and radius of gyration.
+-->
<P>
</DD>
</DL>
<H2><A NAME="SECTION00042000000000000000"></A>
<A NAME="sect:whamoutfiles:output:main"></A>
<BR>
-The structure of the main output file (out)
+The structure of the main output file
</H2>
<P>
<P>
+<!--
<H2><A NAME="SECTION00045000000000000000"></A>
<A NAME="sect:whamoutfiles:histograms"></A>
<BR>
With SEPARATE_PARSET, the PMFs corresponding to different parameter sets are printed to separate files.
<P>
-
+-->
<H2><A NAME="SECTION00047000000000000000"></A>
<A NAME="sect:whamoutfiles:PDB"></A>
<BR>
<P>
The PDB files with names file_[slice_xx_]Tyyy.pdb, where Tyyy specifies a given replica temperature contain the conformations whose probabilities at replica temperature T sum to 0.99, after sorting the conformations
-by probabilities in descending order. The PDB files follow the standard format; see ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf<FONT COLOR="#0000ff">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</FONT>.
+by probabilities in descending order. The PDB files follow the standard format; see <a href="ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</a>.
For single-chain proteins, an example is as follows:
<P>
style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
<div class="hiders" style="display:none" >
-REMD simulation starts from the experimental NMR structure. Secondary
+REMD simulation starts from the experimental NMR structure (the first model
+is taken as the input structure). Secondary
structure restraints are used. Only a short (50 energy evaluations)
initial minimization is requested.
The distance distribution has been downloaded from the SASBDB database (the SASDA25 entry).