<div dir="ltr">OK thank you very much Huan. God bless you.<br><br>On Saturday, July 16, 2016 at 12:19:19 AM UTC+7, hua...@mail.huji.ac.il wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Sorry, I do not have any experience on QM/MM<br><br>On Friday, July 15, 2016 at 2:42:07 PM UTC+3, Dj MG wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Huan, Could you help me find the error part of my qmmm input files?<br><br>On Friday, July 15, 2016 at 3:15:36 PM UTC+7, <a>hua...@mail.huji.ac.il</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Dj MG,<div><br></div><div>As I mentioned in the last reply, the Martyna-Tuckerman (MT) Poisson_solver was proposed for isolated molecules (or clusters). </div><div><br></div><div>That is the same condition as you want to simulate, the protonated water dimer (H3O^+ H2O), which is NOT the periodic system.</div><div><br></div><div>I suggest to read the reference <i>ChemPhysChem</i>, 2011, 12, 1906 - 1915, in which most of the parameters were listed in the Methods section.</div><div><br></div><div>All the best,</div><div>Huan</div><div>.</div><div><br><br>On Thursday, July 14, 2016 at 6:25:13 PM UTC+3, Dj MG wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">OK Huan, i'll try it. Could i know what is the reason you suggestion me to add MT?<br><br>On Thursday, July 14, 2016 at 9:52:45 PM UTC+7, <a>hua...@mail.huji.ac.il</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear DJ MG,<div><br></div><div>The CPK representation only shows the "fixed bond". It is good for the snapshot published in journals, since it is only a picture. However, when displaying your simulation with proton transfer event, the OH bond will break in H3O^+ part and will form a new OH bond in the H2O part. It is a dynamic process. As a result, the "dynamicbond" is more suitable than CPK representation.</div><div><br></div><div>Let's go back to your input file.</div><div><br></div><div>As you said, the system you want to simulate is a dimer cluster. So, in the <font color="#0000ff">&POISSON</font> section, you need to specify the parameter of PERIODIC as NONE, not XYZ. </div><div>In addition, you need to use the Martyna-Tuckerman POSSION_SOLVER, as shown in <a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/POISSON/MT.html" rel="nofollow" target="_blank" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fmanual.cp2k.org%2Ftrunk%2FCP2K_INPUT%2FFORCE_EVAL%2FDFT%2FPOISSON%2FMT.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFkTFswZVnDrG5QL2eXvQS4y1-lbA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fmanual.cp2k.org%2Ftrunk%2FCP2K_INPUT%2FFORCE_EVAL%2FDFT%2FPOISSON%2FMT.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFkTFswZVnDrG5QL2eXvQS4y1-lbA';return true;">https://manual.cp2k.org/<wbr>trunk/CP2K_INPUT/FORCE_EVAL/<wbr>DFT/POISSON/MT.html</a></div><div>This Poisson solver was proposed for the isolated molecules or clusters in the simulation box.</div><div><br></div><div>Keeping the default values for the parameters of ALPHA and REL_CUTOFF would be fine.</div><div><br></div><div>&POISSON</div><div> PERIODIC NONE</div><div> POISSON_SOLVER MT</div><div> &MT</div><div> ALPHA 7.0</div><div> REL_CUTOFF 2.0</div><div> &END MT</div><div>&END POISSON</div><div><br></div><div><br></div><div>In the <font color="#0000ff">QS</font> section, it is better to set EXTRAPOLATION_ORDER as 3. </div><div><br></div><div>In the <font color="#0000ff">&SUBSYS &CELL</font> section, you also need to specify the PERIODIC as NONE, which was not shown in your input file.</div><div>You can try to increase the dimension of your simulation box, perhaps increase to 15.0 angstrom. </div><div><br></div><div> &SUBSYS</div><div> &CELL</div><div> PERIODIC NONE</div><div> ABC 15.0 15.0 15.0</div><div> &END CELL</div><div>...</div><div><br></div><div><br></div><div>I hope those suggestions would be helpful.</div><div><br></div><div>All the best,</div><div>Huan</div><div>.</div><div><br></div><div><br><br>On Thursday, July 14, 2016 at 1:41:44 PM UTC+3, Dj MG wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">OK thank you Huan. I owe you one. I'm beginner in cp2k and english is not my Mother tongue. So that only i can do is try exercises in cp2k website and try and try more. OK i will try your suggestion. And your first suggestion was succeed to change drawing method. My question is why in CPK is failed to visualize the H+ transport?. The fact a lot of journal using CPK model. <br><br>My system is small dimer cluster, any suggestion for this case?<br><br>DJ MG<br>Cheers Always<br><br>On Wednesday, July 13, 2016 at 4:52:11 PM UTC+7, <a>hua...@mail.huji.ac.il</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Dj MG,<div><br></div><div>I checked your files. Actually, the proton has transferred from H3O^+ to H2O in your short trajectory.</div><div><br></div><div>You may use the program called VMD to visualize the position file, which is your "H3O+_H2O-pos-1.xyz". </div><div><br></div><div>By adding the representation with the "Drawing Method" of "dynamicbonds", and setting the "Distance Cutoff" as 1.2, you will be able to observe the proton transfer event.</div><div><br></div><div>The questions in your input file are:</div><div><br></div><div>1) Why you set the "MULTIPLICITY" as 3 in your input file? </div><div>The proton does not have electron, and all electrons in H3O^+ H2O system are in-pair. In my opinion, the multiplicity for this system should be 1.</div><div><br></div><div>2) What kind of system would you like to simulate? Periodic system or just a small dimer cluster?</div><div><br></div><div>3) The temperature printed in your output file fluctuated quite large. The target temperature you set is 313 K, however, as shown in your "H3O+_H2O-1.ener" file, the maximum value even reached to 1339 K, whereas the minimum value dropped down to 99 K. That seems quite unreasonable. You need to choose a better thermostat, like Nose-Hoover chain thermostat or CSVR thermostat.</div><div><br></div><div>All the best,</div><div>Huan</div><div>.</div><div><br><br>On Tuesday, July 12, 2016 at 6:19:40 PM UTC+3, Dj MG wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello cp2k lovers. <br>I have project which aims to simulate proton transfer through grottus mechanism using aimd.<br>I got a problem, why H atoms from H3O+ can't move to H2O?<br>I attached my files below.<br><br><br>Cheers Always<br>...<br></div></blockquote></div></div></blockquote></div></blockquote></div></div></blockquote></div></blockquote></div></div></blockquote></div></blockquote></div></blockquote></div>