<div><br>Hi again !</div>
<div> </div>
<div>Thanks a lot for your help. its a great learning experience since am new to GROMACS.</div>
<div>Well I have made a membrane and i have put two water boxes on top of the membrane.These three structures were combined in to one and i wanted to run energy minimization on the resulting structure.</div>
<div> </div>
<div>I errors i got earlier have vanised when i added the <font size="2">; table-extension = 3.8</font></div>
<div><font size="2">in to my mdp file (thry trial and error). </font></div>
<div><font size="2">i would like to know if this is OK, secondly i get the following outputs after 116 steps </font></div>
<div><font size="2"></font> </div>
<div>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">"Stepsize too small, or no change in energy.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">Converged to machine precision,</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">but not to the requested precision Fmax < 100</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">Double precision normally gives you higher accuracy.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">You might need to increase your constraint accuracy, or turn</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">off constraints alltogether (set constraints = none in mdp file)</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">writing lowest energy coordinates.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">Back Off! I just backed up em.trr to ./#em.trr.9#</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">Back Off! I just backed up emout.pdb to ./#emout.pdb.9#</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">Steepest Descents converged to machine precision in 117 steps,</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">but did not reach the requested Fmax < 100.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">Potential Energy<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>5.4069402e+08</font></span>
</p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">Maximum force<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>3.0060948e+06 on atom 14374
</font></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">Norm of force<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>4.0884328e+07"</font></span>
</p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman"></font></span> </p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman">Below is the copy of my mdp file :</font></span></p><span lang="EN"><font size="2">
<p>;</p>
<p>; User spoel (236)</p>
<p>; Wed Nov 3 17:12:44 1993</p>
<p>; Input file</p>
<p>;</p>
<p>title = Yo</p>
<p>cpp = /usr/bin/cpp</p>
<p>constraints = none</p>
<p>integrator = steep</p>
<p>; ENERGY MINIMIZATION OPTIONS = </p>
<p>; Force tolerance and initial step-size = </p>
<p>emtol = 100</p>
<p>emstep = 0.005</p>
<p>; Max number of iterations in relax_shells = </p>
<p>niter = 20</p>
<p>; Frequency of steepest descents steps when doing CG = </p>
<p>nstcgsteep = 1000</p>
<p>dt = 0.002 ; ps !</p>
<p>nsteps = 5000 ; total 10 ps = 10/0.002.</p>
<p>nstcomm = 1</p>
<p>nstxout = 250</p>
<p>nstvout = 1000</p>
<p>nstfout = 0</p>
<p>nstxtcout = 50</p>
<p>nstlog = 100</p>
<p>nstenergy = 100</p>
<p>nstlist = 10</p>
<p>ns_type = grid</p>
<p>coulombtype = PME</p>
<p>rlist = 1.0</p>
<p>rcoulomb = 1.0</p>
<p>rvdw = 1.0</p>
<p>DispCorr = EnerPres</p>
<p><font size="2">table-extension = 3.8</font></p>
<p>; Berendsen temperature coupling is on in two groups</p>
<p>Tcoupl = berendsen</p>
<p>tc-grps = POP CHO OCH SOL</p>
<p>tau_t = 0.1 0.1 0.1 0.1 </p>
<p>ref_t = 300 300 300 300</p>
<p>; Energy monitoring</p>
<p>energygrps = POP CHO OCH SOL</p>
<p>; Isotropic pressure coupling is now on</p>
<p>Pcoupl = berendsen</p>
<p>Pcoupltype = isotropic</p>
<p>tau_p = 0.5 0.5 0.5</p>
<p>compressibility = 4.5e-5</p>
<p>ref_p = 1.0</p>
<p>; Generate velocites is off at 300 K.</p>
<p>gen_vel = no</p>
<p>gen_temp = 300.0</p>
<p>gen_seed = 173529</p>
<p> Thanks in advance</p>
<p>Kushal</p>
<p> </p></font></span>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman"></font></span> </p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt"><span lang="EN"><font face="Times New Roman"></font></span> </p></div>
<div><span class="gmail_quote">On 4/11/06, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Kushal Seth wrote:<br>> Hi all !<br>> I am running a MD simulation and i got<br><br>You appear to be trying to do an energy minimization, which although
<br>often able to be done by the same code as molecular dynamics, is<br>inherently non-dynamical. Hence it's unwise to confuse matters by<br>referring to one as "MD". See section 1 of the gromacs manual.<br><br>
> "Warning: 1-4 interaction between 1 and 6 at distance 1.102 which is<br>> larger than the 1-4 table size 1.000 nm<br>> These are ignored for the rest of the simulation<br>> This usually means your system is exploding,
<br>> if not, you should increase table-extension in your mdp file"<br><br>It's probably right about that. Look at 1 and 6 in the initial structure<br>and see what you think they should do. Then look at the output of the EM
<br>and see what they have done. This may suggest where the problem lies.<br><br>> and then EM process goes and terminates at 26 th steps saying that<br>><br>> "Stepsize too small, or no change in energy.<br>
> Converged to machine precision,<br>> but not to the requested precision Fmax < 100<br>><br>> Double precision normally gives you higher accuracy.<br>> You might need to increase your constraint accuracy, or turn
<br>> off constraints alltogether (set constraints = none in mdp file)<br>><br>> writing lowest energy coordinates.<br>><br>><br>><br>> Steepest Descents converged to machine precision in 26 steps,<br>
> but did not reach the requested Fmax < 100.<br>> Potential Energy = -6.0066115e+23<br>> Maximum force = 1.8847882e+25 on atom 2502<br>> Norm of force = 5.5707627e+25".<br>><br>> I have tried changing the sizes and pressure
couplings.Thats does not help.<br><br>Pressure coupling can only be applied to a dynamical simulation, so this<br>cannot help at all.<br><br>Check your input structure, your topology, the output structure and your<br>input .mdp file. If the former are all OK and you can't see anything
<br>wrong with the .mdp file, include it in a message here.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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