<div dir="ltr"><div>Hi Marcella,</div><div>I try the MD with periodic and non periodic conditions. When ANGVEL_ZERO was applied for a non periodic cell, the simulation starts with zero angular velocity, but the numerical <span class="gmail-tlid-translation gmail-translation" lang="en"><span title="" class="gmail-">inaccuracies pumps some angular velocity at the first steps... and the molecule starts rotating.</span></span></div><div><span class="gmail-tlid-translation gmail-translation" lang="en"><span title="" class="gmail-">As you mention, for a diatomic molecule it is not possible to apply any constraint... in all cases it will be not physical. <br></span></span></div><div><span class="gmail-tlid-translation gmail-translation" lang="en"><span title="" class="gmail-">Is there a way to fix the rotational movement?<br></span></span> </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El lun., 10 ago. 2020 a las 6:03, Marcella Iannuzzi (<<a href="mailto:marci...@gmail.com">marci...@gmail.com</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">The translational and rotational degrees of freedom are subtracted, hence fixing 4 more degrees of freedom by constraints you end up with a negative number of DoF, which is obviously not physical. <div>Are you using PBC? The ANGVEL_ZERO keyword is ignored with PBC</div><div>Regards</div><div>Marcella</div><div><br><div><br><br></div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Sunday, August 9, 2020 at 10:26:49 PM UTC+2 Lucas Lodeiro wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi all!</div><div><br></div><div>I am exploring single molecule AIMD (H2 in this case) for different purposes. The main problem that I face is temperature/rotational modes. I try to run a AIMD using NVE and NVT ensembles, but there are some problems.</div><div>For an NVE ensemble, the system starts rotating with a conserved angular moment, <span lang="en"><span title="">even if I set equal to zero the total angular moment... This <span lang="en"><span title="">disrupt the linear movement of H2 bond</span></span></span></span> oscillation. The rotation couples with the bond and generates a fake two frequency oscillator. If, after the AIMD, I correct the trajectory to a zero total angular moment for all frames (simple for diatomic homonuclear molecule, but not so easy for polyatomic molecules), the oscillator <span lang="en"><span title="">recovers the single frequency motion.<br></span></span></div><div><span lang="en"><span title="">For an NVT ensemble, the thermalization is so hard for few atoms... and the system is very bad behaved.</span></span></div><div><span lang="en"><span title=""><br></span></span></div><div><span lang="en"><span title="">Now I try an NVE ensemble with constrain MD, fixing the Y and Z position of both atoms, and put the bond along the X direction.</span></span></div><div><span lang="en"><span title=""><br></span></span></div><div><span lang="en"><span title=""> &CONSTRAINT<br> &FIXED_ATOMS<br> COMPONENTS_TO_FIX YZ<br> LIST 1 2<br> &END FIXED_ATOMS<br> &END CONSTRAINT</span></span></div><div><span lang="en"><span title=""><br></span></span></div><div><span lang="en"><span title="">I think with it, I <span><span>force the MD to evolve only over the X axis... but the initial step gives me a NaN temperature and kinetic energy,</span></span></span></span><span lang="en"><span title=""> no matter what initial temperature I use. I attach both files.</span></span></div><div><br></div><div>The output file prints:</div><div> Calculation of degrees of freedom<br> Number of atoms: 2<br> Number of Intramolecular constraints: 4<br> Number of Intermolecular constraints: 0<br> Invariants(translation + rotations): 5<br> Degrees of freedom: -3<br><br><br> Restraints Information<br> Number of Intramolecular restraints: 0<br> Number of Intermolecular restraints: 0<br> ************************** Velocities initialization **************************<br> Initial Temperature NaN K<br> COM velocity: NaN NaN NaN<br> COM position: 5.669178398657 5.669178398657 5.669178398657<br> Angular velocity: NaN NaN NaN<br> *******************************************************************************</div><div><br></div><div>It seems, the degrees of freedom is: 3N - constrains - invariants...</div><div>Is there a way to force the MD only along one axis to avoid rotation?</div><div><br></div><div>Regards!<br></div><div><span lang="en"><span title=""></span></span><span></span><span></span><span lang="en"><span title=""><span><span></span></span></span></span></div></div>
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