<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Dear GMX users,</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> I am facing problem while
doing energy minimization before the molecular dynamic simulation step of a system
consisting of protein, membrane, water and 14 ions. </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">The minim.mdp file is as follows</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">-------------------------------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">; minim.mdp - used as input into
grompp to generate em.tpr</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">; Parameters describing what to
do, when to stop and what to save</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">integrator<span> </span>= steep<span> </span>;
Algorithm (steep = steepest descent minimization)</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">emtol<span> </span>= 1000.0<span> </span><span> </span>; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">emstep<span> </span>= 0.01<span> </span>; Energy step size</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">nsteps<span> </span>= 50000<span> </span><span> </span><span> </span>;
Maximum number of (minimization) steps to perform</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">; Parameters describing how to
find the neighbors of each atom and how to calculate the interactions</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">nstlist<span> </span>= 1<span> </span><span> </span>; Frequency to update the neighbor list and
long range forces</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">ns_type<span> </span>= grid<span> </span>;
Method to determine neighbor list (simple, grid)</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">rlist<span> </span>= 1.2<span> </span><span> </span>; Cut-off for making neighbor list (short
range forces)</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">coulombtype<span> </span>= PME<span> </span>;
Treatment of long range electrostatic interactions</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">rcoulomb<span> </span>= 1.2<span> </span>;
Short-range electrostatic cut-off</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">rvdw<span> </span>= 1.2<span> </span>;
Short-range Van der Waals cut-off</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">pbc<span> </span>= xyz <span> </span>; Periodic Boundary Conditions</span><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><b><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">---------------------------------------------------------------------------------------------------------</span></b></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">when I run this using the command </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><b><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></b></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><b><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">grompp –f minim_1.mdp –c system_inflated.gro
topol.top –o em.tpr </span></b><span style="font-size:12.0pt;font-family:"Times New Roman","serif""></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> then I invoked mdrun which
gave following error</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">--------------------------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Reading file topol.tpr, VERSION 4.0.7 (single
precision)</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Loaded with Money</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Steepest Descents:</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>Tolerance
(Fmax)<span> </span>=<span> </span>1.00000e+03</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>Number of
steps<span> </span>=<span> </span>50000</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Step=<span> </span>14,
Dmax= 1.2e-06 nm, Epot=<span> </span>3.03531e+22
Fmax=<span> </span>inf, atom= 1417</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Stepsize too small, or no change in energy.</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Converged to machine precision,</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">but not to the requested precision Fmax < 1000</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Double precision normally gives you higher accuracy.</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">You might need to increase your constraint accuracy,
or turn</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">off constraints alltogether (set constraints = none
in mdp file)</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">writing lowest energy coordinates.</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Steepest Descents converged to machine precision in
15 steps,</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">but did not reach the requested Fmax < 1000.</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Potential Energy<span>
</span>=<span> </span>3.0353124e+22</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Maximum force<span>
</span>=<span> </span>inf on atom 1417</span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"">Norm of force<span>
</span>=<span> </span>inf</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">-----------------------------------------------------------------</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">After this I changed the </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">emstep<span> </span>= 0.1<span>
</span>; Energy step size</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">nsteps<span> </span>= 5000<span> </span>; Maximum number of (minimization) steps to
perform</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">constraints<span> </span>= none</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">After these changes the no of steps
increased to 18 but still the system did not converge and potential energy is
very high</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">----------------------------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Reading file em.tpr, VERSION 4.0.7
(single precision)</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Loaded with Money</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Steepest Descents:</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><span>
</span>Tolerance (Fmax)<span> </span>=<span> </span>1.00000e+03</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><span>
</span>Number of steps<span> </span>=<span> </span>5000</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Step=<span> </span>17, Dmax= 1.5e-06 nm, Epot=<span> </span>3.03531e+22 Fmax=<span> </span>inf, atom= 1417</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Stepsize too small, or no change in
energy.</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Converged to machine precision,</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">but not to the requested precision
Fmax < 1000</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Double precision normally gives you
higher accuracy.</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">You might need to increase your
constraint accuracy, or turn</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">off constraints alltogether (set
constraints = none in mdp file)</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">writing lowest energy coordinates.</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Steepest Descents converged to
machine precision in 18 steps,</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">but did not reach the requested Fmax
< 1000.</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Potential Energy<span> </span>=<span>
</span>3.0353124e+22</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Maximum force<span> </span>=<span> </span>inf on atom 1417</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Norm of force<span> </span>=<span> </span>inf</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">----------------------------------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">What changes can I do in my minim.mdp
file to converge my system and get a negative value of Epot.</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">The topol.top file looks </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">--------------------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">[ system ]</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">; Name</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">protein</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">128-Lipid DPPC Bilayer </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">[ molecules ]</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">; Compound<span> </span>#mols</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Protein_A<span> </span>1</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">DPPC<span> </span>121</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">SOL<span> </span>11107</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">CL- <span> </span>14</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">-----------------------------------------------------------------------------------------------------</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Thanks,</span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">Parul </span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif""> </span></p>