[gmx-users] trjconv -pbc mol/nojump

2011-12-11 Thread leila karami
Hi, You should use trjconv in 2 steps: (1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_pbc_nojump.xtc -pbc nojump in this step, select system for output (2) trjconv_d -s md_100ns.tpr -f md_100ns_pbc_nojump.xtc -o md_100ns_pbc_mol_center.xtc -pbc mol -center in this step, select sol

Re: [gmx-users] trjconv -pbc mol/nojump

2011-12-11 Thread 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.p

[gmx-users] trjconv -pbc mol/nojump

2011-12-11 Thread 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