[gmx-users] trjconv -pbc mol/nojump

[Efrat Exlrod]

Hi,



I have run simulation of a large solute in a box of water. Trying to look at the simulation output I used trjconv with and without the -pbc nojump option.



For example:

(1)  trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_noPBC_pbcmol.pdb -pbc mol -ur compact

(2)  trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_noPBC_nojump.pdb -pbc nojump



With pbc=mol the solute is broken to few pieces, while the water molecules are placed in a box with few holes. With pbc=nojump the solute seems reasonably well but the water molecules are scattered in a large radius around the solute, and some of them are not broken (OH or H).



I tried many options of trjconv and read the 'suggested trjconv workflow' but I still can't obtain a reasonable complete system after the simulation.



How can I solve this problem?



Thanks, Efrat


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