Thanks for the reply Justin,
This is how I added the position restraint in topology -------------------------------------------------------------------------- ; Include DPPC chain topology #include "dppc.itp" #ifdef POSRES_LIPID ; Position restraint for each lipid #include "lipid_posre.itp" #endif -------------------------------------------------------------------------- And this is how the define statement is in .mdp file -------------------------------------------------------------------------- title = Simulated Annealing for B3-DPPC define = -DPOSRES -DPOSRES_LIPID ; restrain protein and lipid P8 -------------------------------------------------------------------------- Maybe there is some problem I am not able to figure. Thanks. Parul Parul tew wrote: > Dear Gmx users, > > > > I am working on a transmembrane protein and my system contains protein, DPPC > > bilayer, water (spc) and ions. After adding ions I energy minimized the > system and used trjconv to remove periodicity. In the equilibration It is unnecessary to manipulate the output file at this stage. Be sure you're not doing anything funny to the coordinates that cause the problem described below. > phase the lipid molecules were entering the voids in the solvent leaving > the protein naked. So, I used position restraint on the Z-plane and > restrained the phosphate head (atom 8) and one carbon atom on each tail > (atoms 31, 50 with a force constant of 1,000 kJ mol/−/1 nm/−/2. > > ----------------------------------------------------------- > > ; position restraint file for DPPC > > > > [ position_restraints ] > > ; i funct fcx fcy fcz > > 8 1 0 0 1000 > > 31 1 0 0 1000 > > 50 1 0 0 1000 > > > > ----------------------------------------------------------- > > But after running a simulated annealing for 500ps I get a distorted > lipid membrane where the lipids tend to pack at one end but open at the > other end of the box. > > After this I had put position restraint on all the atoms of the lipid on > the z-plane and again tried the simulated annealing but it gave the same > result. > > I am not able to understand where I am going wrong. > The fact that none of the approaches is working suggests to me that either the topology does not #include the position restraint file or you do not have the proper "define" statement in your .mdp file. A simple restraint on P8 in the Z-dimension should prevent distortions; I use such a technique routinely. -Justin
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