I want to relax the guanine molecule but the relaxed structure show some hydrogens detached from the main structure (see graph attached). It looks like there is some sort of interaction between the periodic image even I put it in a big box. Please, I will appreciate any suggestions.
Wudmir PhD student, UK. - - - - - - - - - - - - - - - - - - - - - - - - Input - - - - - - - - - - - - - &CONTROL title = ' guanine ', calculation = 'relax', restart_mode = 'from_scratch', tprnfor = .TRUE., etot_conv_thr = 1.D-4, prefix = 'gua-relax-22-06-a' pseudo_dir = '~/espresso-pseudo/' outdir = './' &SYSTEM ibrav = 0, celldm(1) = 18.897259886, nat = 16, ntyp = 4 ecutwfc = 25.0, ecutrho = 200.0, occupations='smearing', smearing='gaussian', degauss=0.01 / &ELECTRONS / &IONS / ATOMIC_SPECIES C 12.0107 C.pbe-mt_fhi.UPF O 15.9994 O.pbe-mt_fhi.UPF H 1.00794 H.pbe-mt_fhi.UPF N 14.0067 N.pbe-mt_fhi.UPF K_POINTS gamma CELL_PARAMETERS (alat) 8.000 0.000 0.00 0.000 8.000 0.00 0.000 0.000 8.00 ATOMIC_POSITIONS (angstrom) N 0 0 0 C 0 0 1.440908 C 1.357081 0 1.91969 C 2.396462 0 0.987468 N 2.338369 0 -0.36805 C 1.102405 0 -0.817435 N 0.886377 0 -2.16208 N 1.849196 0 3.211795 C 3.148326 0 3.067635 N 3.542068 0 1.739303 H -0.032303 0 -2.567841 H 1.694052 0 -2.761628 H -0.932932 0 -0.393625 O -1.065793 0 2.031419 H 3.871687 0 3.871397 H 4.482237 0 1.373635 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140626/ace40eb0/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: g-relax.jpg Type: image/jpeg Size: 12477 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140626/ace40eb0/attachment.jpg
