On 11/12/2011 11:23 PM, Efrat Exlrod wrote:
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?
This is a straightforward situation where the suggested workflow works:
remove jumps (so all molecules are whole), then center on the solute,
and then put everything in some box (so -pbc mol, which leaves the
centered solute where it is).
Mark
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