Ok, here's my topology file:<div><br></div><div><div>; Include forcefield parameters</div><div>#include "ffgmx.itp"</div><div>#include "lipid.itp"</div><div><br></div><div>; Include Lipid Topologies</div>
<div>#include "popc.itp"</div><div><br></div><div>; Include water topology</div><div>#include "spc.itp"</div><div><br></div><div>#ifdef POSRES_WATER</div><div>; Position restraint for each water oxygen</div>
<div>[ position_restraints ]</div><div>; i funct fcx fcy fcz</div><div> 1 1 1000 1000 1000</div><div>#endif</div><div><br></div><div>; Include generic topology for ions</div><div>
#include "ions.itp"</div><div><br></div><div>[ system ]</div><div>; Name</div><div>Berger Membrane in water</div><div><br></div><div>[ molecules ]</div><div>; Compound #mols</div><div>POP 128</div>
<div>SOL 2460</div><div><br></div><div>and here's my ff_dum.itp:</div><div><br></div><div><div>; These constraints are used for dummy constructions as generated by pdb2gmx.</div><div>; Values depend on the details of the forcefield, vis. bondlengths and angles</div>
<div>; These parameters are designed to be used with the GROMACS forcefields</div><div>; ffgmx and ffgmx2 and with the GROMOS96 forcefields G43a1, G43a2 and G43b1.</div><div><br></div><div>; Constraints for the rigid NH3/CH3 groups depend on the hygrogen mass,</div>
<div>; since an increased hydrogen mass translates into increased momentum of</div><div>; inertia which translates into a larger distance between the dummy masses.</div><div>#ifdef HEAVY_H</div><div>; now the constraints for the rigid NH3 groups</div>
<div>#define DC_MNC1 0.175695</div><div>#define DC_MNC2 0.188288</div><div>#define DC_MNMN 0.158884</div><div>; now the constraints for the rigid CH3 groups</div><div>#define DC_MCN 0.198911</div><div>#define DC_MCS 0.226838</div>
<div>#define DC_MCC 0.204247</div><div>#define DC_MCNR 0.199798</div><div>#define DC_MCMC 0.184320</div><div>#else</div><div>; now the constraints for the rigid NH3 groups</div><div>#define DC_MNC1 0.144494</div><div>#define DC_MNC2 0.158002</div>
<div>#define DC_MNMN 0.079442</div><div>; now the constraints for the rigid CH3 groups</div><div>#define DC_MCN 0.161051</div><div>#define DC_MCS 0.190961</div><div>#define DC_MCC 0.166809</div><div>#define DC_MCNR 0.162009</div>
<div>#define DC_MCMC 0.092160</div><div>#endif</div><div>; and the angle-constraints for OH and SH groups in proteins:</div><div>#define DC_CS 0.23721</div><div>#define DC_CO 0.19849</div><div>#define DC_PO 0.21603</div>
<div><br></div><div>Thanks for your help!</div><div>Gard</div></div></div>