<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt"><br><span id="result_box" class="" lang="en"><span class="hps"><span id="result_box" class="" lang="en"><span class="hps">Thank you for</span> <span class="hps">answers</span></span><br><br>I</span> <span class="hps">think the problem</span> <span class="hps">was resolved</span> <span class="hps">after</span> <span class="hps">increasing the size</span> <span class="hps">of the</span> <span class="hps">cell</span> <span class="hps">in</span> <span class="hps">2</span> <span class="hps">borh</span><span>,</span> <span class="hps">so I</span> <span class="hps">understand the</span> <span class="hps">possible</span> <span class="hps">cause</span> <span class="hps">of the problem</span><span>:</span> <span class="hps">somehow the molecules</span> <span class="hps">were interacting</span> <span
class="hps">with</span> <span class="hps">its own</span> <span class="hps">image</span> <span class="hps">(that</span> <span class="hps">makes sense</span><span>?</span><span>)</span><span>,</span></span><span class="hps"> when I</span> <span class="hps">used a</span> <span class="hps">non-free program</span> <span id="result_box" class="" lang="en"><span class="hps atn">(</span><span class="">HyperChem</span> <span class="hps">::::</span> <span class="hps">he performed</span> <span class="hps atn">a pre-</span><span class="">optimization</span> <span class="hps">with</span> <span class="hps">periodic</span> <span class="hps">boundary</span> <span class="hps">conditions</span><span class="hps"></span><span class="">) this problem has</span> <span class="hps">not</span> <span class="hps">happened</span><span class=""></span></span><span></span>. <span class="hps">Now, the question</span> <span class="hps">is to maintain</span> <span class="hps">a more
realistic</span> density. <span id="result_box" class="" lang="en"><span class=""></span><span class="hps">However</span><span class="">, I'm</span> <span class="hps">relieved</span></span><br><br>Best regards<span id="result_box" class="" lang="en"><span></span></span><span id="result_box" class="" lang="en"><span></span></span><span id="result_box" class="" lang="en"><span class="hps"></span></span><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;">Muito obrigado a todos.<br></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif;
background-color: transparent; font-style: normal;"><br><span></span></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><span>Alex W. F. Borges</span><br><span id="result_box" class="short_text" lang="en"><span class="hps">Theoretical</span> <span class="hps">chemistry</span> <span class="hps">student</span></span></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><span>Goiânia - Brazil</span></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><span><br></span></div><div style="display: block;" class="yahoo_quoted">
<br> <br> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10pt;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> Em Quinta-feira, 28 de Novembro de 2013 14:16, Paolo Giannozzi <paolo.giannozzi@uniud.it> escreveu:<br> </font> </div> <blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; margin-top: 5px; padding-left: 5px;"> <div class="y_msg_container">Just in case: try with other pseudopotentials. I haven't <br clear="none">heard any complaints about HGH pseudopotentials, but I <br clear="none">cannot rule out problems in the conversion to UPF format.<br clear="none">have you tried simple systems first?<br clear="none"><br clear="none">Paolo<br clear="none"><div class="yqt3034316734" id="yqtfd35884"><br clear="none">On Thu, 2013-11-28 at 05:43
-0800, Alex wrote:<br clear="none">> Dear user QE.<br clear="none">> <br clear="none">> <br clear="none">> I'm using cp.x to perform molecular dynamics of one of bulk water<br clear="none">> molecules with asparagine.<br clear="none">> Following protocol, I minimized the function of wave electronics with<br clear="none">> stationary nuclei.<br clear="none">> <br clear="none">> <br clear="none">> However, in the second stage, during the optimization of the geometry<br clear="none">> (with damp for electrons and ions) <br clear="none">> the water molecules take a non-real geometry, in which one side of the<br clear="none">> molecule, the OH distance becomes 1.98 angstrorn (A).<br clear="none">> The opposite side, has the normal size of the bond which is 0.97 A. I<br clear="none">> confess that since I started using it very often, <br clear="none">> and sometimes does not, but do not know why that. Sometimes
change is<br clear="none">> functional and that resolved, sometimes not.<br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> Incoherent bond distances of water after geometry optmization >>>>><br clear="none">> H------------------O -----------H<br clear="none">> (sorry by bad graphic)<br clear="none">> | 1.98 A| |0.97 A|<br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> Can someone help me? <br clear="none">> Put my input to be analyzed.<br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> &CONTROL<br clear="none">> title = 'Asp0s'<br
clear="none">> calculation = 'cp',<br clear="none">> restart_mode = 'restart',<br clear="none">> ndr = 51 !already minimized wf with sd for electrons and<br clear="none">> ions=none.<br clear="none">> ndw = 52, <br clear="none">> nstep = 50000,<br clear="none">> iprint = 1, <br clear="none">> isave = 10,<br clear="none">> tstress = .TRUE.,<br clear="none">> tprnfor = .TRUE.,<br clear="none">> dt = 5.0d0,<br clear="none">> etot_conv_thr = 1.d-8,<br clear="none">> ekin_conv_thr = 1.d-4,<br clear="none">> forc_conv_thr = 1.d-4,<br clear="none">> prefix = 'asp'<br clear="none">> pseudo_dir = 'pseudo/'<br clear="none">> outdir = './'<br clear="none">> /<br clear="none">> <br clear="none">> <br clear="none">> &SYSTEM<br
clear="none">> ibrav = 1, <br clear="none">> celldm(1) = 20, <br clear="none">> celldm(2) = 0.0, <br clear="none">> celldm(3) = 0.0, <br clear="none">> celldm(4) = 0.0, <br clear="none">> celldm(5) = 0.0, <br clear="none">> celldm(6) = 0.0, <br clear="none">> nat = 122,<br clear="none">> ntyp = 4,<br clear="none">> ecutwfc = 70.0,<br clear="none">> /<br clear="none">> <br clear="none">> <br clear="none">> &ELECTRONS<br clear="none">> emass = 400.d0,<br clear="none">> emass_cutoff = 2.5d0,<br clear="none">> orthogonalization = 'ortho',<br clear="none">> electron_dynamics = 'damp',<br clear="none">> electron_damping = 0.1<br clear="none">> ortho_max = 500,<br clear="none">> !electron_temperature = 'not_controlled',<br clear="none">> !electron_velocities =
'zero'<br clear="none">> /<br clear="none">> <br clear="none">> <br clear="none">> &IONS<br clear="none">> ion_dynamics = 'damp',<br clear="none">> ion_damping = 0.01,<br clear="none">> !ion_nstepe = 10,<br clear="none">> !ion_temperature = 'nose',<br clear="none">> !tempw = 350,<br clear="none">> !fnosep = 70,<br clear="none">> !ion_velocities = 'zero'<br clear="none">> /<br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> ATOMIC_SPECIES<br clear="none">> <br clear="none">> <br clear="none">> O 16.0d0 O.pbe-hgh.UPF<br clear="none">> H 1.0d0 H.pbe-hgh.UPF <br clear="none">> C 12.0d0 C.pbe-hgh.UPF <br clear="none">> N 14.0d0 N.pbe-hgh.UPF<br clear="none">> <br clear="none">> <br clear="none">> ATOMIC_POSITIONS {angstrom}<br
clear="none">> <br clear="none">> <br clear="none">> C -0.244144 1.783022 -1.335832 <br clear="none">> C -2.567204 -0.241389 5.783803 <br clear="none">> N -1.038197 -1.652589 5.418683 <br clear="none">> C -6.336078 -1.532299 -1.532562 <br clear="none">> O -5.122808 -0.424258 -2.279843 <br clear="none">> N 3.987336 0.412822 -1.692063 <br clear="none">> C 0.552282 -0.043486 0.368085 <br clear="none">> O 1.73575 0.043368 0.476670 <br clear="none">> O
1.126133 -1.181319 1.757325 <br clear="none">> H -0.844512 -1.781630 -0.580034 <br clear="none">> H -1.992345 -1.968023 0.581635 <br clear="none">> H -1.547999 -0.018973 1.618910 <br clear="none">> H -1.017864 1.793541 0.067225 <br clear="none">> H -2.180408 0.669590 -0.675764 <br clear="none">> H 1.490782 1.185685 -2.387313 <br clear="none">> H 1.070763 1.992771 -0.909308 <br clear="none">> H 0.490233 -1.888235 1.458829 <br clear="none">>
O 5.160929 1.400891 -4.018523 <br clear="none">> H 5.585303 1.845186 -4.767840 <br clear="none">> H 5.903707 1.074826 -3.488501 <br clear="none">> O 6.523016 -2.630620 -1.333026 <br clear="none">> H 6.731773 -1.730291 -1.624223 <br clear="none">> H 6.238875 -2.519196 -0.413345 <br clear="none">> ( ........)<br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> Alex.<br clear="none">> Thanks to all.</div><br clear="none">> _______________________________________________<br clear="none">> Pw_forum mailing list<br clear="none">> <a
shape="rect" ymailto="mailto:Pw_forum@pwscf.org" href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br clear="none">> <a shape="rect" href="http://pwscf.org/mailman/listinfo/pw_forum" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br clear="none"><br clear="none">-- <br clear="none"> Paolo Giannozzi, Dept. Chemistry&Physics&Environment, <br clear="none"> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br clear="none"> Phone +39-0432-558216, fax +39-0432-558222 <div class="yqt3034316734" id="yqtfd27289"><br clear="none"><br clear="none"></div><br><br></div> </blockquote> </div> </div> </div> </div></body></html>