Dear all, Dear Justin,This time I want to ask the gurus about this problem I encountered in the Equilibration step of my system made of 3 individual (small) protein chains in a solvated DMPC bilayer, no ions present since the protein system is neutral...
Following the tutorial I started with make_ndx_d -f em_after_solv.gro -o index_after_solv.ndx for which I got the following list: ----------------------------------------------------------------- Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 129 Protein residues There are: 123 Other residues There are: 3215 Water residues Analysing Protein...Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
0 System : 16649 atoms 1 Protein : 1346 atoms 2 Protein-H : 1025 atoms 3 C-alpha : 129 atoms 4 Backbone : 387 atoms 5 MainChain : 519 atoms 6 MainChain+Cb : 636 atoms 7 MainChain+H : 649 atoms 8 SideChain : 697 atoms 9 SideChain-H : 506 atoms 10 Prot-Masses : 1346 atoms 11 non-Protein : 15303 atoms 12 Other : 5658 atoms 13 DMPC : 5658 atoms 14 Water : 9645 atoms 15 SOL : 9645 atoms 16 non-Water : 7004 atoms -----------------------------------------------------Since I did not add ions I have formed a (merged) group named SOL_SOL after chosing 15 | 15 , and another merged group named Protein_DMPC by choosing 1 | 13...
Next, I started the NVT equilibration with:grompp_d -f nvt.mdp -c em_after_solv.gro -p topol_mod_lip_solv.top -n index_after_solv.ndx -o nvt.tpr
The nvt.mpd file is the same as the one given in the tutorial, the only changes I made were:
tc-grps = Protein DMPC SOL_SOL and comm-grps = Protein_DMPC SOL_SOL After this I ran mdrun_mpi_d -v -deffnm nvtWhen this process is finished I looked at the resulting nvt.gro file and found the following:
1) The 3 protein chains complex is fine, at the center of the box as it should be, but 2) The 2 DMPC layer are separated (splitted) leaving a large gap between them forming a )( shape where the top and bottom of this figure contain one layer of DMPC plus water molecules, while in the narrow section the protein complex is found... In the void between the two DMPC layers no water molecules are present... Very odd!...
Please advice... Cheers, Ramon Garduno
<<attachment: ramon.vcf>>
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