Hi, <div><br></div><div>I have uploaded related files to the thread. Please check.</div><div><br></div><div>Yu<br><br><br><blockquote name="replyContent" class="ReferenceQuote" style="padding-left:5px;margin-left:5px;border-left:#b6b6b6 2px solid;margin-right:0">-----Original Messages-----<br>
<b>From:</b><span id="rc_from">"Mark Abraham" <mark.j.abraham@gmail.com></span><br>
<b>Sent Time:</b><span id="rc_senttime">2017-11-25 23:50:46 (Saturday)</span><br>
<b>To:</b> gmx-developers@gromacs.org<br>
<b>Cc:</b> GMX-developer <gromacs.org_gmx-developers@maillist.sys.kth.se><br>
<b>Subject:</b> Re: [gmx-developers] Fw: [GROMACS - Bug #2301] (Rejected) Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'<br><br><div dir="ltr">Hi,<div><br></div><div>Thanks for the message. Please do see the thread on Redmine - Berk has already realized that he misunderstood an aspect, and is seeking more information in order to see if we have something to fix.</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Sat, Nov 25, 2017 at 2:51 PM Du, Yu <<a href="mailto:duyu@sioc.ac.cn" target="_blank">duyu@sioc.ac.cn</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear GMX Developers and Prof. Hess, <div><br></div><div><div><span style="font-size:14px">I have said in the previous redmine post that I didn't change the temperature coupling. Both nvt and nvt2 use </span><span style="font-size:14px">nose-hoover thermostat.</span></div><div><br>I don't think this rejection is acceptable. If you need some additional information, please let me know.</div><div><br></div><div>Thanks.</div><div><br></div><div>Yu</div><div><br></div><div>--<br>Du, Yu<br>PhD Student,<br>Shanghai Institute of Organic Chemistry<div>345 Ling Ling Rd., Shanghai, China. </div><div>Zip: 200032, <span style="font-size:14px">Tel: (86) 021 5492 5275</span></div><div><span style="font-size:14px"><br></span></div><blockquote class="m_6415510724385086238ReferenceQuote" style="padding-left:5px;margin-left:5px;border-left:#b6b6b6 2px solid;margin-right:0">
-----Original Messages-----<br>
<b>From:</b><span id="m_6415510724385086238rc_from"><a href="mailto:admin@redmine.gromacs.org" target="_blank">admin@redmine.gromacs.org</a></span><br>
<b>Sent Time:</b><span id="m_6415510724385086238rc_senttime">2017-11-25 04:30:22 (Saturday)</span><br>
<b>To:</b> <br>
<b>Cc:</b> <br>
<b>Subject:</b> [GROMACS - Bug #2301] (Rejected) Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'<br><br>
Issue <a href="http://redmine.gromacs.org/issues/2301#change-15383" style="color:#169" target="_blank">#2301</a> has been updated by Berk Hess.
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<ul class="m_6415510724385086238journal m_6415510724385086238details" style="color:#959595;margin-bottom:1.5em">
<li><strong>Status</strong> changed from <i>New</i> to <i>Rejected</i></li>
</ul>
<p>gmx grompp -h tells that -e is for read temperature (and pressure) coupling variables. Because you change the temperature coupling algorithm the variables changes (the types, not values), so you get an error.</p>
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<h1 style="font-family:"Trebuchet MS",Verdana,sans-serif;margin:0px;font-size:1.3em;line-height:1.4em"><a href="http://redmine.gromacs.org/issues/2301#change-15383" style="color:#169" target="_blank">Bug #2301: Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'</a></h1>
<ul class="m_6415510724385086238details" style="color:#959595;margin-bottom:1.5em"><li><strong>Author: </strong>Yu Du</li>
<li><strong>Status: </strong>Rejected</li>
<li><strong>Priority: </strong>Normal</li>
<li><strong>Assignee: </strong>Yu Du</li>
<li><strong>Category: </strong>preprocessing (pdb2gmx,grompp)</li>
<li><strong>Target version: </strong></li>
<li><strong>Affected version - extra info: </strong></li>
<li><strong>Affected version: </strong>2016.4</li>
<li><strong>Difficulty: </strong>uncategorized</li></ul>
<p>I want to choose the last N frames from nvt-normal2.trr as starting coordinates and velocities.</p>
<p><code style="font-family:Consolas,Menlo,"Liberation Mono",Courier,monospace">gmx grompp -quiet -f nvt.mdp -c nvt-normal2.gro -t nvt-normal2.trr -time 8 -e nvt-normal2.edr -p topol.top -n index.ndx -o nvt-8.tpr</code></p>
<p>I didn't change the thermostat and grompp errors are shown below.</p>
<p>NOTE 1 [file nvt.mdp]:<br> The group cutoff scheme is deprecated since GROMACS 5.0 and will be<br> removed in a future release when all interaction forms are supported for<br> the verlet scheme. The verlet scheme already scales better, and it is<br> compatible with GPUs and other accelerators.</p>
<p>Setting the LD random seed to -1655106643<br>Generated 2628 of the 2628 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 2628 of the 2628 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'LIG'<br>turning H bonds into constraints...<br>Excluding 3 bonded neighbours molecule type 'Protein_chain_A'<br>turning H bonds into constraints...<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>turning H bonds into constraints...<br>Excluding 1 bonded neighbours molecule type 'NA'<br>turning H bonds into constraints...<br>Number of degrees of freedom in T-Coupling group Protein_LIG is 15018.52<br>Number of degrees of freedom in T-Coupling group Water_and_ions is 79806.48<br>Reading Coordinates, Velocities and Box size from old trajectory<br>Will read till time 8<br>trr version: GMX_trn_file (single precision)<br>Reading frame 8 time 8.000 Using frame at t = 8 ps<br>Starting time for run is 0 ps<br>Opened nvt-normal2.edr as single precision energy file<br>Reading energy frame 8 time 8.000</p>
<p>-------------------------------------------------------<br>Program: gmx grompp, version 2016.4<br>Source file: src/gromacs/fileio/enxio.cpp (line 1146)</p>
<p>Fatal error:<br>Could not find energy term named 'Xi-0-Protein_LIG'</p>
<p>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a class="m_6415510724385086238external" href="http://www.gromacs.org/Documentation/Errors" style="color:#169" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------</p>
<p>P.S. nvt.mdp:</p>
<p>; Run parameters<br>integrator = md-vv<br>tinit = 0<br>nsteps = 5000 ; 10ps<br>dt = 0.002</p>
<p>; Output parameters<br>nstxout = 500<br>nstvout = 500<br>nstfout = 500<br>nstenergy = 500<br>nstlog = 500<br>nstxout-compressed = 500<br>energygrps = Protein LIG</p>
<p>; Neighbor searching<br>nstlist = 5 <br>ns-type = grid<br>pbc = xyz<br>rlist = 1.1<br>cutoff-scheme = group</p>
<p>; Electrostatics and VdW<br>coulombtype = pme<br>rcoulomb = 1.1<br>vdwtype = cut-off<br>rvdw = 1.1</p>
<p>; Temperature coupling<br>Tcoupl = nose-hoover<br>tc-grps = Protein_LIG Water_and_ions<br>tau_t = 1.0 1.0<br>ref_t = 300 300</p>
<p>; Pressure coupling<br>Pcoupl = no</p>
<p>; Velocity generation<br>gen_vel = no</p>
<p>; Bond parameters<br>continuation = yes<br>constraints = h-bonds<br>constraint-algorithm = lincs<br>lincs-order = 6<br>lincs-iter = 2</p>
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