GROMACS version: 2020.4
GROMACS modification: Yes/No
Here post your question
I would like to construct bilayer consisting of DOPC with both the double bonds of acyl chains in trans configuration. In this context, I have created first cis configuration of DOPC (which is the default configuration) using Charmm GUI and then changed the dihedral restraints in DOPC.itp to 180 degrees as follows:
#ifdef DIHRES
[ dihedral_restraints ]
25 36 28 30 1 -120.0 2.5 DIHRES_FC
60 63 65 67 1 180.0 0.0 DIHRES_FC
107 110 112 114 1 180.0 0.0 DIHRES_FC
And then ran energy minimization (using -DPOSRES -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0) using steepest descent algorithm. I have tried different combinations of CG and SD as well. However, I am unable to resolve the error due to LINCS warning. I understand the error is due to poor starting structure. Can someone help me in resolving the issue or guide me alternative way of packing and creating the trans bilayer system. I have tried packmol and memgen but am facing similar issue.