<div dir="ltr">Hello Jeurg,<div>Thank you for your reply. If it is special case for SCP-NDDO (PNNL), how about for PM3 and PM6 methods? (Paper includes PM3, PM6 and SCP-NDDO methods) I performed SE-MD calculation (NVT) with PM3 using whatever the controls mentions in the paper, but O-H bond lengths increases too much (more than 3 angstrom). I think I am missing something in the input file.</div> <div> </div><div>I will use PNNL method also and see what happens.</div><div> </div><div>Thank you.</div><div> </div><div>Bharat Sharma</div></div><div class="gmail_extra"> <div class="gmail_quote">On Wed, Feb 19, 2014 at 11:53 AM, <<a href="mailto:hut...@chem.uzh.ch" target="_blank">hut...@chem.uzh.ch</a>> wrote: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi that paper uses a special NDDO version adapted for periodic systems. To do such a calculation you need a section like this &DFT &QS METHOD PNNL &SE SCP T INTEGRAL_SCREENING SLATER &END &END QS &SCF &OUTER_SCF # TYPE SCP EPS_SCF 1.0E-8 MAX_SCF 20 &END OUTER_SCF SCF_GUESS ATOMIC EPS_SCF 1.0E-8 MAX_SCF 20 &OT T MINIMIZER DIIS SCP_NDDO T PRECONDITIONER FULL_ALL &END OT &END SCF &END DFT regards Juerg Hutter -------------------------------------------------------------- Juerg Hutter Phone : ++41 44 635 4491 Institut für Chemie FAX : ++41 44 635 6838 Universität Zürich E-mail: <a href="mailto:hut...@chem.uzh.ch">hut...@chem.uzh.ch</a> Winterthurerstrasse 190 CH-8057 Zürich, Switzerland --------------------------------------------------------------- -----<a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a> wrote: ----- To: <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a> From: bharat Sent by: <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a> Date: 02/18/2014 09:07PM Subject: [CP2K:4957] SE MD in CP2K <div class="HOEnZb"><div class="h5"> Hello Everyone, I am trying to reproduce the results published on J. Phy. Chem. A by G. Murdachaew et al. (<a href="http://pubs.acs.org/doi/abs/10.1021/jp110481m" target="_blank">http://pubs.acs.org/doi/abs/10.1021/jp110481m</a>). I used the similar control parameters described in the paper. The simulation is for 64 water molecules. After 30 steps, structure is terribly going wrong. O-H distance increases too much (>3Angstrom). The initial coordinates are used from <a href="http://pubs.acs.org/doi/abs/10.1021/jz401931f" target="_blank">http://pubs.acs.org/doi/abs/10.1021/jz401931f</a>. Please find input file, output file, and dcd file here. <a href="https://drive.google.com/folderview?id=0B56PcAs22G9NdEd4eWh3ekFTd3c&usp=sharing" target="_blank">https://drive.google.com/folderview?id=0B56PcAs22G9NdEd4eWh3ekFTd3c&usp=sharing</a> Can anyone help me to figure out where I am doing wrong? Thank you. Bharat @SET CURR_I 01 #@SET SEED 1000 &EXT_RESTART RESTART_FILE_NAME ./wt_bk_AM101-1.restart &END EXT_RESTART &GLOBAL PROGRAM_NAME CP2K PROJECT_NAME wt_bk_AM1${CURR_I} RUN_TYPE MD # SEED ${SEED} PREFERRED_FFT_LIBRARY FFTW # ECHO_INPUT YES PRINT_LEVEL LOW SAVE_MEM &END GLOBAL &MOTION # &PRINT # &FORCES # FORMAT XMOL # &END FORCES # &END PRINT &MD ENSEMBLE NVT STEPS 10000 TIMESTEP 0.50 TEMPERATURE 300 &THERMOSTAT TYPE NOSE REGION MASSIVE &NOSE LENGTH 3 YOSHIDA 3 TIMECON 100 MTS 2 &END NOSE &END THERMOSTAT &THERMAL_REGION &PRINT &TEMPERATURE &EACH MD 1 &END EACH &END TEMPERATURE &END PRINT &END THERMAL_REGION &PRINT &ENERGY &EACH MD 1 &END EACH &END ENERGY &END PRINT &END MD &PRINT &RESTART &EACH MD 1 &END EACH &END RESTART &RESTART_HISTORY OFF &END RESTART_HISTORY &TRAJECTORY LOW FORMAT DCD &EACH MD 1 &END EACH &END TRAJECTORY &VELOCITIES OFF &END VELOCITIES &FORCES &END FORCES &END PRINT &END MOTION &FORCE_EVAL METHOD QS &DFT &SCF SCF_GUESS ATOMIC EPS_SCF 1.0E-7 MAX_SCF 5000 &OUTER_SCF MAX_SCF 10 &END OUTER_SCF &OT # Mingshun's scheme for PM6 PRECONDITIONER FULL_SINGLE_INVERSE MINIMIZER DIIS N_DIIS 9 &END OT &PRINT &RESTART &EACH MD 1 &END EACH &END RESTART &RESTART_HISTORY OFF &END RESTART_HISTORY &END PRINT &END SCF &QS METHOD PM3 # My scheme EPS_DEFAULT 1.0E-12 EXTRAPOLATION ASPC EXTRAPOLATION_ORDER 3 &SE # &PARAMETER # @INCLUDE PARAM # &END PARAMETER &COULOMB CUTOFF 10.0 RC_RANGE 0.5 # RC_TAPER 2 &END COULOMB &SCREENING RC_RANGE 0.5 &END SCREENING &LR_CORRECTION CUTOFF 6.0 RC_RANGE 0.5 &END LR_CORRECTION &EXCHANGE CUTOFF 8.0 RC_RANGE 0.5 &END EXCHANGE &END SE &END QS &MGRID COMMENSURATE # CUTOFF 280 &END MGRID &POISSON POISSON_SOLVER PERIODIC PERIODIC XYZ &EWALD &MULTIPOLES MAX_MULTIPOLE_EXPANSION QUADRUPOLE &END MULTIPOLES EWALD_TYPE EWALD ALPHA 0.5 GMAX 31 &END EWALD &END POISSON &PRINT &E_DENSITY_CUBE &EACH MD 1 &END EACH &END E_DENSITY_CUBE &END PRINT &END DFT &SUBSYS &CELL ABC 12.4138 12.4138 12.4138 PERIODIC XYZ &END CELL &COORD ........................................ ......................................... ........................................ ....................................... ........................................ &END COORD &END SUBSYS &END FORCE_EVAL -- You received this message because you are subscribed to the Google Groups "cp2k" group. 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Visit this group at <a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/group/cp2k</a>. For more options, visit <a href="https://groups.google.com/groups/opt_out" target="_blank">https://groups.google.com/groups/opt_out</a>. </div></div></blockquote></div> </div>