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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Did you look at atom 2073?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>liaoxyi<br>
<b>Sent:</b> Wednesday, 12 October 2011 3:59 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Implicit solvent problems<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="ZH-CN" style="font-family:"Times New Roman","serif";color:black">Hi, dear all,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ZH-CN" style="font-family:"Times New Roman","serif";color:black">I</span><span lang="ZH-CN" style="color:black">’</span><span lang="ZH-CN" style="font-family:"Times New Roman","serif";color:black">m doing the simulation involved
in protein and some surface.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ZH-CN" style="font-family:"Times New Roman","serif";color:black">I encounter this problem when trying to use implicit solvent</span><span style="font-family:"Times New Roman","serif";color:black"> model with GMX4.5.3.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">First, minimize. When doing this I got the result as below:</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 0, Dmax= 1.0e-02 nm, Epot= -1.91727e+06 Fmax= 6.19542e+06, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 1, Dmax= 1.0e-02 nm, Epot= -1.99260e+06 Fmax= 1.05712e+06, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 2, Dmax= 1.2e-02 nm, Epot= -2.09734e+06 Fmax= 1.79058e+05, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 4, Dmax= 7.2e-03 nm, Epot= -2.17474e+06 Fmax= 7.22113e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 6, Dmax= 4.3e-03 nm, Epot= -2.17724e+06 Fmax= 4.33926e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 8, Dmax= 2.6e-03 nm, Epot= -2.18069e+06 Fmax= 3.24778e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 10, Dmax= 1.6e-03 nm, Epot= -2.18404e+06 Fmax= 2.76114e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 13, Dmax= 4.7e-04 nm, Epot= -2.18500e+06 Fmax= 2.63803e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 17, Dmax= 7.0e-05 nm, Epot= -2.18514e+06 Fmax= 2.62045e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 19, Dmax= 4.2e-05 nm, Epot= -2.18522e+06 Fmax= 2.61000e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 22, Dmax= 1.3e-05 nm, Epot= -2.18524e+06 Fmax= 2.60689e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 23, Dmax= 1.5e-05 nm, Epot= -2.18527e+06 Fmax= 2.60315e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 27, Dmax= 2.3e-06 nm, Epot= -2.18527e+06 Fmax= 2.60258e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Step= 29, Dmax= 1.4e-06 nm, Epot= -2.18488e+06 Fmax= 2.60222e+04, atom= 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Stepsize too small, or no change in energy.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Converged to machine precision,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:#993300">but not to the requested precision Fmax < 1000</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Double precision normally gives you higher accuracy.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">writing lowest energy coordinates.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Steepest Descents converged to machine precision in 30 steps,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">but did not reach the requested Fmax < 1000.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Potential Energy = -2.1852700e+06</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Maximum force = 2.6025840e+04 on atom 2073</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Norm of force = 2.2667976e+03</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">---------------------------------------</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">From above, the force is extremely large. And I don</span><span lang="ZH-CN" style="color:black">’</span><span style="font-family:"Times New Roman","serif";color:black">t know
why.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">the minim.mdp is as below:</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">; minim.mdp - used as input into grompp to generate em.tpr</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">; Parameters describing what to do, when to stop and what to save</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">integrator = steep ; Algorithm (steep = steepest descent minimization)</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">emstep = 0.01 ; Energy step size</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">nsteps = 50000 ; Maximum number of (minimization) steps to perform</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">; Parameters describing how to find the neighbors of each atom and how to calculate the interactions</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">nstlist = 1 ; Frequency to update the neighbor list and long range forces</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">ns_type = grid ; Method to determine neighbor list (simple, grid)</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">rlist = 1.0 ; Cut-off for making neighbor list (short range forces)</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">coulombtype = Cut-off ; for Implicit solvent long-range electrostatics</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">rcoulomb = 1.0 ; Short-range electrostatic cut-off</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">rvdw = 1.0 ; Short-range Van der Waals cut-off</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">pbc = xyz ; Periodic Boundary Conditions (yes/no)</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">; implicit_solvent</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">implicit_solvent = GBSA</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">gb_algorithm = OBC</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">nstgbradii = 1</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">rgbradii = 1.0</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">gb_epsilon_solvent = 78.3</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">gb_obc_alpha = 1 ; OBC(II)</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">gb_obc_beta = 0.8 ; OBC(II)</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">gb_obc_gamma = 4.85 ; OBC(II)</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">gb_dielectric_offset = 0.09</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">-----------------</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Is there any item that</span><span lang="ZH-CN" style="color:black">’</span><span style="font-family:"Times New Roman","serif";color:black">s not proper or needed to add?</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Is the minimization necessary for implicit solvent?
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Thank you again for your reading.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";color:black">Kiara</span><span style="color:black"><o:p></o:p></span></p>
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