Hello,<br><br>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:<br><br><br>There are 0 atoms and 0 charges for free energy perturbation <br>
Removing pbc first time<br><br>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).<br>
<p class="PreformattedText" style="text-align: justify;"><span style="">EM</span></p>
<p class="PreformattedText" style="text-align: justify;"><span style="">grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o
em-l0.tpr >& output.grompp_em</span></p>
<p class="PreformattedText" style="text-align: justify;"><span style="">mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g<span style=""> </span>em-l0.log -e em-l0.edr -v >&
output.mdrun_em</span></p>
<p class="PreformattedText" style="text-align: justify;"><span style="">MD</span></p>
<p class="PreformattedText" style="text-align: justify;"><span style="">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</span></p>
<p class="PreformattedText" style="text-align: justify;"><span style="">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</span></p>
<br><br><span style=""> PE60-0c-itp.top is:</span><br>==========================<br>; Include forcefield parameters<br>#include "ffoplsaa.itp"<br><br>#include "Hexane-0c.itp"<br><br>[ moleculetype ]<br>
; Name nrexcl<br>Polymer 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 opls_135 1 EthB C1 1 0 12.011 ; qtot 0<br>
2 opls_140 1 EthB H11 1 0 1.008 ; qtot 0<br> 3 opls_140 1 EthB H12 1 0 1.008 ; qtot 0<br> 4 opls_140 1 EthB H13 1 0 1.008 ; qtot 0<br>
5 opls_136 1 EthB C2 2 0 12.011 ; qtot 0<br><br>.<br>.<br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>Polymer<br><br>[ molecules ]<br>
; Compound #mols<br>Polymer 4<br>Hexane 480 <br>=======================================<br><br>Please help me what wrong is...<br><br>Thanks<br>moeed<br>