<div style="text-align: left;">This is likely an embarrassingly trivial problem, but let's see.<br><br>I am following the energy minimization scheme presented in the groningen tutorial<br><br><a href="http://md.chem.rug.nl/education/mdcourse/MDpract.html">http://md.chem.rug.nl/education/mdcourse/MDpract.html</a><br>
<br>I believe I follow the directions exactly, yet I can not minimize below Fmax~500<br><br>I download 1AKI, as in the tutorial, <br>I issue<br><br>pdb2gmx -f 1AKI.pdb <br>grompp -f minim.mdp <br>mdrun -v<br><br>and I use the mdp file<br>
<br>"<pre><font size="4">title = Minimization of Hen Egg White Lysozyme (1AKI.pdb) Title of run<br><br>; The following lines tell the program the standard locations where to find certain files<br>cpp = /lib/cpp Preprocessor<br>
include = -I../top Directories to include in the topology format<br><br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep Algorithm (steep = steepest descent minimization)<br>emtol = 1.0 Stop minimization when the maximum force < 1.0 kJ/mol<br>
nsteps = 200 Maximum number of (minimization) steps to perform<br>nstenergy = 10 Write energies to disk every nstenergy steps<br>nstxtcout = 10 Write coordinates to disk every nstxtcout steps<br>xtc_grps = Protein Which coordinate group(s) to write to disk<br>
energygrps = Protein Which energy group(s) to write to disk<br><br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>nstlist = 5 Frequency to update the neighbor list and long range forces<br>
ns_type = simple Method to determine neighbor list (simple, grid)<br>rlist = 1.0 Cut-off for making neighbor list (short range forces)<br>coulombtype = cut-off Treatment of long range electrostatic interactions<br>
rcoulomb = 1.0 long range electrostatic cut-off<br>rvdw = 1.0 long range Van der Waals cut-off<br>constraints = none Bond types to replace by constraints<br>pbc = no Periodic Boundary Conditions (yes/no)"<br>
</font></pre><font size="4"><br><font size="2">I tried multiple choices of potentials and I tried gromacs 3.3.2, 3.3.3 and cvs, with single and double precision. They all finish with the same output(except single finishes in fewer steps)<br>
<br>"Step= 57, Dmax= 3.2e-11 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478<br>Step= 60, Dmax= 9.6e-12 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478<br>Step= 62, Dmax= 5.8e-12 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478<br>
Step= 65, Dmax= 1.7e-12 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478<br>Step= 67, Dmax= 1.0e-12 nm, Epot= -9.45085e+03 Fmax= 8.07834e+02, atom= 478<br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>
but not to the requested precision Fmax < 1<br><br>writing lowest energy coordinates.<br><br>Back Off! I just backed up confout.gro to ./#confout.gro.5#<br><br>Steepest Descents converged to machine precision in 68 steps,<br>
but did not reach the requested Fmax < 1.<br>Potential Energy = -9.59521978368287e+03<br>Maximum force = 8.07834306442108e+02 on atom 478<br>Norm of force = 1.49469417798063e+02<br>"<br><br>This seems unreasonably high. Are there some obvious mistakes people make that result in this kind of behavior? I have tried multiple pdb structure and none of them can minimize below fmax~100. I have also tried l-bfgs and cg. None of them can converge to the request precision. <br>
<br>thanks<br><br>-Paul<br></font></font></div>