Hello, I tried to follow the FE tutorials and get my own system working but it seems I am missing something coz I get a blank dgdl file. log file is saying:
There are 0 atoms and 0 charges for free energy perturbation Removing pbc first time What I do is running EM (lambda 0) on a solvated system which is already equilibrated (and density is obtained by NPT) followed by a MD NVT since density has to be fixed. My guess is I am making mistake in combining itp file of hexane into polymer (solute). EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr >& output.grompp_em mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v >& output.mdrun_em MD grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n PE-HEX.ndx>& output.grompp_md mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x md-l0.xtc -dgdl md-l0.dgdl -v >& output.mdrun_md PE60-0c-itp.top is: ========================== ; Include forcefield parameters #include "ffoplsaa.itp" #include "Hexane-0c.itp" [ moleculetype ] ; Name nrexcl Polymer 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_135 1 EthB C1 1 0 12.011 ; qtot 0 2 opls_140 1 EthB H11 1 0 1.008 ; qtot 0 3 opls_140 1 EthB H12 1 0 1.008 ; qtot 0 4 opls_140 1 EthB H13 1 0 1.008 ; qtot 0 5 opls_136 1 EthB C2 2 0 12.011 ; qtot 0 . . ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Polymer [ molecules ] ; Compound #mols Polymer 4 Hexane 480 ======================================= Please help me what wrong is... Thanks moeed
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