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On 8/11/2011 3:17 AM, Steven Neumann wrote:
<blockquote
cite="mid:CAKZJqQGpqWX_9OmEXfsu8qV-N1BOYbUwUnu5mZZ93=Wx7X1O3g@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Mon, Nov 7, 2011 at 2:26 PM, Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px
0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>
<br>
Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px
0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im">Dear Gmx Users,<br>
I know that this problem has been discussed may times but
I cannot find the solution to get rid of pbc in my system:
protein and ligand. I followed the workflow:<br>
<br>
1. First make your molecules whole if you want them
whole<br>
<br>
trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o
mdwhole.xtc<br>
<br>
2. Cluster your molecules/particles if you want them
clustered<br>
<br>
3. Extract the first frame from the trajectory as
reference for removing jumps if you want to remove jumps.<br>
<br>
trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb<br>
<br>
4. Remove jumps if you want to have them removed
using the first frame<br>
<br>
trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o
mdwholeNOjump.xtc<br>
<br>
</div>
5. Center your system using some criterion. Doing so
shifts the system, so don't use |trjconv -|pbc| nojump|
after this step.
<div class="im"><br>
<br>
trjconv -f mdwholeNOjump.xtc -center -o
mdwholeNOjumpCENTER.xtc<br>
<br>
6. Put everything in some box.<br>
<br>
trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o
mdwholeNOjumpCENTERbox.xtc<br>
<br>
7. Fit if desired and don't use any PBC related
option afterwards.<br>
<br>
trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit
rot+trans -o mdfinal.xtc<br>
<br>
<br>
I used SYSTEM everywhere as output orinput. However, my
ligand is still jumping like a fly around the stable
protein. Do you have any suggestions?<br>
<br>
<br>
</div>
</blockquote>
<br>
Center on either the protein, the ligand, or some custom index
group of residues surrounding the ligand. Centering on the
whole system usually doesn't do anything useful.<br>
<br>
-Justin<br>
<br>
</blockquote>
<div> </div>
<div>Thank you guys but...</div>
<div> </div>
<div>I am trying and it does not work... my ligand is jumping
like an idiot outside the box changing its position even two
dimensions of box in one frame. </div>
</div>
</blockquote>
<br>
I have no idea what you mean by this.<br>
<br>
<blockquote
cite="mid:CAKZJqQGpqWX_9OmEXfsu8qV-N1BOYbUwUnu5mZZ93=Wx7X1O3g@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>I removed -ur compact from the first line and I tried
centering on ligand or protein (centering group: LIG or
Protein, output: SYSTEM). No results... </div>
<div>My ligand at the begining of the simualtion is not within
the protein. Please, help :(((( I tried this workflow with
many ligands and same protein - it worked! Now it does not...</div>
</div>
</blockquote>
<br>
Sure. So far you've given us no understanding of what your ligand is
doing during the simulation. If you don't know either, go and look
at it. Then go and look at the trajectory from each stage of your
work flow and see what it looks like and how things are changing.
Then when something looks wrong you have a single step you can
trouble shoot... maybe the operation is not sensible, maybe the way
you did it is wrong, maybe the code is wrong.<br>
<br>
You cannot expect to transfer work flows from another simulation
without considering what is happening in this one. Scenarios where
your ligand is diffusing away from your protein and reassociating to
another side require different work flows from one where the ligand
stays nearby a binding pocket. In the latter, you should probably
use -pbc cluster in step 2, though some of the time it won't matter.
In the former, using -nojump to allow diffusion out of the box, and
then step 6 to put everything back in the box doesn't make sense.
Just doing operations and selecting groups without considering the
nature of the operation will get a garbage result. There's a good
reason mdrun doesn't attempt to second-guess how you would like all
of this done!<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKZJqQGpqWX_9OmEXfsu8qV-N1BOYbUwUnu5mZZ93=Wx7X1O3g@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>Here is my workflow:</div>
<div> </div>
<div>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
class="MsoNormal"><font face="Times New Roman"><span
style="mso-list: Ignore"><font size="3">1.</font><span
style="FONT: 7pt 'Times New Roman'"> </span></span><font
size="3">First make your molecules whole if you want
them whole.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
mso-margin-bottom-alt: auto" class="MsoNormal"><span
style="COLOR: red"><font size="3"><font face="Times New
Roman">trjconv -f md.trr -s md.tpr -pbc whole -o
mdwhole.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
class="MsoNormal"><font face="Times New Roman"><span
style="mso-list: Ignore"><font size="3">2.</font><span
style="FONT: 7pt 'Times New Roman'"> </span></span><font
size="3">Cluster your molecules/particles if you want
them clustered</font></font></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
class="MsoNormal"><font face="Times New Roman"><span
style="mso-list: Ignore"><font size="3">3.</font><span
style="FONT: 7pt 'Times New Roman'"> </span></span><font
size="3">Extract the first frame from the trajectory as
reference for removing jumps if you want to remove
jumps.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
mso-margin-bottom-alt: auto" class="MsoNormal"><span
style="COLOR: red"><font size="3"><font face="Times New
Roman">trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o
1stframe.pdb</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
class="MsoNormal"><font face="Times New Roman"><span
style="mso-list: Ignore"><font size="3">4.</font><span
style="FONT: 7pt 'Times New Roman'"> </span></span><font
size="3">Remove jumps if you want to have them removed
using the first frame (system)</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
mso-margin-bottom-alt: auto" class="MsoNormal"><span
style="COLOR: red"><font size="3"><font face="Times New
Roman">trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc
nojump -o mdwholeNOjump.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
class="MsoNormal"><font face="Times New Roman"><span
style="mso-list: Ignore"><font size="3">5.</font><span
style="FONT: 7pt 'Times New Roman'"> </span></span><font
size="3">Center your system using some criterion. Doing
so shifts the system, so don't use </font></font><code><span
style="FONT-SIZE: 10pt">trjconv -</span></code><span
class="highlight"><span style="BACKGROUND: yellow"><font
face="Times New Roman" size="3">pbc</font></span></span><code><span
style="FONT-SIZE: 10pt"> nojump</span></code><font
face="Times New Roman" size="3"> after this step (tried
centering on LIG or PROTEIN)</font></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
class="MsoNormal"><span style="COLOR: red"><font size="3"><font
face="Times New Roman">trjconv -f mdwholeNOjump.xtc -n
Ligand.ndx -center -o mdwholeNOjumpCENTER.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
class="MsoNormal"><font face="Times New Roman"><span
style="mso-list: Ignore"><font size="3">6.</font><span
style="FONT: 7pt 'Times New Roman'"> </span></span><font
size="3">Put everything in some box.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
mso-margin-bottom-alt: auto" class="MsoNormal"><span
style="COLOR: red"><font size="3"><font face="Times New
Roman">trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6
-o mdwholeNOjumpCENTERbox.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt;
mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;
mso-list: l0 level1 lfo1; tab-stops: list 54.0pt"
class="MsoNormal"><font face="Times New Roman"><span
style="mso-list: Ignore"><font size="3">7.</font><span
style="FONT: 7pt 'Times New Roman'"> </span></span><font
size="3">Fit if desired and don't use any <span
class="highlight"><span style="BACKGROUND: yellow">PBC</span></span>
related option afterwards.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto;
mso-margin-bottom-alt: auto" class="MsoNormal"><span
style="COLOR: red"><font size="3"><font face="Times New
Roman">trjconv -f mdwholeNOjumpCENTERbox.xtc -s
1stframe.pdb -fit rot+trans -o mdfinal.xtc</font></font></span></p>
<span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt;
mso-fareast-font-family: 'Times New Roman';
mso-ansi-language: EN-GB; mso-fareast-language: EN-GB;
mso-bidi-language: AR-SA">With point three, the issue is
that <a moz-do-not-send="true" title="Documentation/Gromacs
Utilities/trjconv"
href="http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv">trjconv</a>
removes the jumps from the first frame using the reference
structure provided with </span><code><span
style="FONT-SIZE: 10pt; mso-ansi-language: EN-GB;
mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">-s</span></code><span
style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt;
mso-fareast-font-family: 'Times New Roman';
mso-ansi-language: EN-GB; mso-fareast-language: EN-GB;
mso-bidi-language: AR-SA">. If the reference structure (run
input file) is not clustered/whole, </span><code><span
style="FONT-SIZE: 10pt; mso-ansi-language: EN-GB;
mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">trjconv
-</span></code><span class="highlight"><span
style="FONT-FAMILY: 'Times New Roman'; BACKGROUND: yellow;
FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New
Roman'; mso-ansi-language: EN-GB; mso-fareast-language:
EN-GB; mso-bidi-language: AR-SA">pbc</span></span><code><span
style="FONT-SIZE: 10pt; mso-ansi-language: EN-GB;
mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">
nojump</span></code><span style="FONT-FAMILY: 'Times New
Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New
Roman'; mso-ansi-language: EN-GB; mso-fareast-language:
EN-GB; mso-bidi-language: AR-SA"> will undo steps 1 and</span></div>
<div> </div>
<div>Steven</div>
<div> </div>
<div> </div>
<div>========================================<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 moz-do-not-send="true" href="http://vt.edu/"
target="_blank">vt.edu</a> | <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080" target="_blank"
value="+15402319080">(540) 231-9080</a><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
======================================== </div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px
0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>
<div class="h5"><br>
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