Steered MD again

guys compared different pulling rates

Steered MD in GROMACS (pull code)

The pull code allows to apply a force between two centers of mass (for >1 groups). It appears to be useful to simulate protein penetration into lipid membrane (channel formation). Config must have a following lines:
pull_start = yes
pull_init1 = 0
pull = umbrella
pull_geometry = direction
pull_group0 = Protein
pull_group1 = POPC
pull_vec1 = 0 0 0.5
pull_k1 = 3000
pull_rate1 = 0.01 ; nm/ps Extreme parameters for extreme pulling

discussions: [1], [2]

transmembrane protein modeling pt. 2

Protein-lipid_bilayer system generated with Schroedinger`s Desmond gives too large bilayer hole, which can contain water molecules after solvation. Some manuals recommended to make a local vdwradii.dat copy with modified C radius (0.5 [0.15 is default]). But 0.5 appears to be not enough (0.6 was used).

The Desmond Membrane Builder fuckup lies in fact that I can manually implement protein into membrane more accurately, but having more brainfucking post-processing. So it goes.

transmembrane protein modeling

Lipid topology (.itp required for GROMACS MD simulations) contains 52 atoms. But lipid bilayer PDB structure consists of (>52)-atom molecules (such a difference is a result of using united-atom force field) with all hydrogens, which were considered in GROMOS96 53a6 FF. It was obtained 52-atom molecules system with:

cat lipid.pdb | grep -v "0.00 H" > lipid-noH.pdb

Output PDB format details depends on software:

mdrun -deffnm box-min -c box-min.pdb -v -nice 0 # output is box-min.pdb [box-min.tpr assumed to be exist]

mdrun -deffnm box-min -c box-min.gro -v -nice 0 # output is box-min.gro

vmd box-min.gro # box-min.gro was converted to box-min(from_gro).pdb with vmd

spdbv box-min.pdb # warning 1: at least one HETATM group lacked proper CONNECT informations. Connection will be generated between atoms that are closer than 2.000A, which can generate false bonds. [CONNECT section was removed manually] warning 2: File ignored (either or is not a valid PDB file, or it contains only a Carbon Alpha trace). => spdbv doesn`t understand GROMACS PDB output

spdbv box-min(from_gro).pdb #warning 1: the same; => successfully opened