Fragment-Based Energy Calculation for C2H6O1 in Complex Structures
This guide provides a detailed approach to creating a fragment input file for complex structures featuring C2H6O1. It outlines steps including the removal of specific atoms from fragments, saving new compositions, and editing stoichiometry matrices. It also discusses running calculations using QCISD and SCF methods in a computational chemistry setup. By following these procedures, users can efficiently run energy difference calculations and manage fragment libraries on a cluster, facilitating precise molecular modeling workflows.
Fragment-Based Energy Calculation for C2H6O1 in Complex Structures
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Presentation Transcript
Complexes Whattodo? Howtodo?
Energydifference C2_H6_N0_O1_F0_S0 • ECOMPLEX – (EFRAGMENT1 + EFRAGMENT2) + O1_H2_112 C2_H4_112 C2_H6_N0_O1_F0_S0_123
Create an fragment input file • Remove atoms of fragement1 (O1_H2) from complex • New composition save in name (.com) • C2_H4_112 • Edit file: put a new stochiometry matrix in to input 4 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
INPUT SAMPLE C2_H4_112 # G3MP2B3 Opt(Cartesian,Tight,CalcAll,MaxStep=1,MaxCycles=300) QCISD=MaxCyc=200 SCF(XQC) NoSymm 4 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 C -1.00483800 -1.79070600 1.72274100 C -0.64747700 -2.49626200 2.72377700 H -4.57960384 -0.26330764 1.66514964 H -2.33214300 0.12309600 -0.40487900 H -1.50385600 2.03708500 -1.26587400 H -1.18616800 0.95853300 -2.32526200
Enthalpydifference C2_H6_N0_O1_F0_S0 • HCOMPLEX – (HFRAGMENT1 + HFRAGMENT2) + O1_H2_112 C2_H4_112 C2_H6_N0_O1_F0_S0_123
RUNS • Create a libraryonclusterunder project library: …/fragments • Create a library …/fragments/start • Uploadallinputs of fragmentsinto: …/fragments/start • Start thecalcs! • Script should be startedfrom …/fragements library
