[gmx-users] trjconv -pbc mol/nojump

[Mark Abraham]

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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