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<p>Dear all,</p>
<p> </p>
<p>Apologies for getting back to this topic again - am still having trouble trying to get distance restraints to work on my protein.</p>
<p> </p>
<p>Following Tsjerk's advice, I have </p>
<p>1)put the tpr file through gmxdump: </p>
<p> disre = No<br>
disre_weighting = Conservative<br>
disre_mixed = FALSE<br>
dr_fc = 10000</p>
<p>2)there was no distance restraint information on the edr file (no surprise considering the above)</p>
<p> </p>
<p>I have then tried inserting "disre = simple" in my mdp file and attempted to run the simulation.
</p>
<p>mpisub 1 test.jif </p>
<p>(note that 1 = 8 cpus)</p>
<p>Unfortunately, I got the following error:</p>
<p>Fatal error:<br>
There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 11.8602 nm<br>
Change the number of nodes or mdrun option -rdd or -dds<br>
Look in the log file for details on the domain decomposition<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></p>
<p> </p>
<p>I also tried changing the number of cpus</p>
<p>mpisub 2 test.jif </p>
<p>(2=16 cpus)</p>
<p>The error was</p>
<p>Fatal error:<br>
There is no domain decomposition for 10 nodes that is compatible with the given box and a minimum cell size of 11.8602 nm<br>
Change the number of nodes or mdrun option -rdd or -dds<br>
Look in the log file for details on the domain decomposition<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
</p>
<p>I dont understand why the error stated 10 instead of 16 nodes. Removing "disre=simple" will allow the simulation to run smoothly. Can anyone enlighten me on how to apply distance restraints properly?</p>
<p> </p>
<p>Many thanks.</p>
<p> </p>
<p>Huiwen</p>
<div style="FONT-FAMILY: Times New Roman; COLOR: #000000; FONT-SIZE: 16px">
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<div style="DIRECTION: ltr" id="divRpF288894"><font color="#000000" size="2" face="Tahoma"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of NG HUI WEN [HuiWen.Ng@nottingham.edu.my]<br>
<b>Sent:</b> 18 January 2012 16:40<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> RE: [gmx-users] questions on distance restraints<br>
</font><br>
</div>
<div></div>
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<div class="WordSection1">
<p class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'; COLOR: #1f497d; FONT-SIZE: 11pt">Dear Tsjerk,</span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'; COLOR: #1f497d; FONT-SIZE: 11pt"></span> </p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'; COLOR: #1f497d; FONT-SIZE: 11pt">Thanks very much indeed for confirming this, really appreciate it. I will do as you suggest to have a more thorough check.
</span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'; COLOR: #1f497d; FONT-SIZE: 11pt"></span> </p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'; COLOR: #1f497d; FONT-SIZE: 11pt">Best wishes,</span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'; COLOR: #1f497d; FONT-SIZE: 11pt">Huiwen</span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'; COLOR: #1f497d; FONT-SIZE: 11pt"></span> </p>
<div style="BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<p class="MsoNormal"><b><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt">From:</span></b><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>Tsjerk Wassenaar<br>
<b>Sent:</b> Wednesday, January 18, 2012 1:08 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] questions on distance restraints</span></p>
</div>
<p class="MsoNormal"> </p>
<p>Hi Huiwen,</p>
<p>Your approach seems good. Information about the distance restraints will be printed in the log file from mdrun, or can be extracted from the .edr file. You can also work your way through the information in the .tpr file given by gmxdump to see if they are
indeed properly defined.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<blockquote style="MARGIN-TOP: 5pt; MARGIN-BOTTOM: 5pt">
<p style="MARGIN-BOTTOM: 12pt" class="MsoNormal">On Jan 18, 2012 1:46 AM, "NG HUI WEN" <<a href="mailto:HuiWen.Ng@nottingham.edu.my" target="_blank">HuiWen.Ng@nottingham.edu.my</a>> wrote:</p>
<div>
<div>
<p class="MsoNormal">Dear gmxusers,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I have some questions about distance restraints that I hope you would be able to shed some light on. Thanks in advance.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I am trying to apply distance restraints to my protein. Below was what I did:</p>
<p> </p>
<p class="MsoNormal">-use genrestr to create my ca_disre.itp<br>
genrestr –f membedded_em.gro –o ca_disre.itp –disre (pop-up prompt: CA atoms selected)</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">-in my mdp file</p>
<p class="MsoNormal">I added this line near the top: </p>
<p class="MsoNormal">define = -DDISRES</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">-my top file looks like that</p>
<p class="MsoNormal">; Include forcefield parameters</p>
<p class="MsoNormal">#include "gromos53a6_lipid.ff/forcefield.itp"</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">;Include Protein Topology</p>
<p class="MsoNormal">#include "A2a.itp"</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">; Include Position restraint file</p>
<p class="MsoNormal">#ifdef DISRES</p>
<p class="MsoNormal">#include "ca_disre.itp"</p>
<p class="MsoNormal">#endif</p>
<p class="MsoNormal">;</p>
<p class="MsoNormal">#ifdef POSRES</p>
<p class="MsoNormal">#include "posre.itp"</p>
<p class="MsoNormal">#endif</p>
<p class="MsoNormal">;</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">;Include POPC topology</p>
<p class="MsoNormal">#include "popc.itp"</p>
<p class="MsoNormal">#ifdef LIPID_POSRES</p>
<p class="MsoNormal">#include "lipid_posre.itp"</p>
<p class="MsoNormal">#endif</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">;Include water topology</p>
<p class="MsoNormal">#include "gromos53a6_lipid.ff/spc.itp"</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">#ifdef POSRES_WATER</p>
<p class="MsoNormal">; Position restraint for each water oxygen</p>
<p class="MsoNormal">[ position_restraints ]</p>
<p class="MsoNormal">; i funct fcx fcy fcz</p>
<p class="MsoNormal"> 1 1 1000 1000 1000</p>
<p class="MsoNormal">#endif</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">; Include topology for ions</p>
<p class="MsoNormal">#include "gromos53a6_lipid.ff/ions.itp"</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">[ system ]</p>
<p class="MsoNormal">; Name</p>
<p class="MsoNormal">Protein and POPC and Water </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">[ molecules ]</p>
<p class="MsoNormal">; Compound #mols</p>
<p class="MsoNormal">Protein_chain_X 1</p>
<p class="MsoNormal">POPC 327</p>
<p class="MsoNormal">SOL 24767</p>
<p class="MsoNormal">CL 11</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">The simulation ran without a problem. However, after it was completed, I compared the final protein structure with the initial and it looked like the atoms (even the CA atoms , especially those in the loops) had moved quite a fair bit away
from the original position. This made me wonder if the distance restraints had indeed been applied or perhaps the force constant was not large enough (default =1000 kJ/mol/nm^2)? I had checked the mdout.mdp file “define = -DDISRES” was there… wasn’t sure
how else I could check this.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">To test whether it was due to the latter, I had tried rerunning the simulation for 1ns simulation with “disre_fc = 10000” added to the mdp file. This time the atoms did not move as far away as previously observed.
</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I have tried google-ing for the proper way to impose distance restraints but didn’t find my searches too useful. I wonder if anyone could confirm with me that the above method is correct/ tell me that I had done something wrong.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Cheers for that!</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Best wishes,</p>
<p class="MsoNormal">Huiwen</p>
<p class="MsoNormal"> </p>
<p style="MARGIN-LEFT: 0.25in" class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
</div>
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