Re: [gmx-users] regarding pbc issue

On 1/17/18 12:06 PM, Rose wrote: Thank you so much,I've got it now. we know that for example 2 molecule can not stick to each other they just close enough till repulse each other. Now, imagine pulling, if I can not see "really broken" structures in classicalMD , so what would be my

Re: [gmx-users] regarding pbc issue

Thank you so much,I've got it now. we know that for example 2 molecule can not stick to each other they just close enough till repulse each other. Now, imagine pulling, if I can not see "really broken" structures in classicalMD , so what would be my criterion and clue to say that:"that's

Re: [gmx-users] regarding pbc issue

On 1/17/18 11:23 AM, Rose wrote: I mean, sometimes structures may really break or collapse, in these situations trjconv won't show these broken structures whole yes? just will show them broken (as they really are) yes? In the context of the question I was answering, "broken" means that it

Re: [gmx-users] regarding pbc issue

I mean, sometimes structures may really break or collapse, in these situations trjconv won't show these broken structures whole yes? just will show them broken (as they really are) yes? Sent from my iPhone > On Jan 17, 2018, at 18:15, Justin Lemkul wrote: > > > >> On

Re: [gmx-users] regarding pbc issue

On 1/17/18 9:40 AM, Rose wrote: You mean if -pbc could make molecule whole,everything is ok, but if not it means the molecule was broken from first, yes? mdrun writes "broken" coordinates because the physics does not depend on our visualization convenience. Most programs account for PBC.

Re: [gmx-users] regarding pbc issue

You mean if -pbc could make molecule whole,everything is ok, but if not it means the molecule was broken from first, yes? Sent from my iPhone > On Jan 17, 2018, at 16:19, Justin Lemkul wrote: > > > >> On 1/17/18 5:51 AM, Vidya R wrote: >> Hi Justin, >> >> I got the same

Re: [gmx-users] regarding pbc issue

On 1/17/18 5:51 AM, Vidya R wrote: Hi Justin, I got the same result as you said. What confused me was, when I viewed movie.pdb file generated by the following command, gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n index.ndx -o movie.pdb two hydrogen molecules of

Re: [gmx-users] regarding pbc issue

Hi Justin, I got the same result as you said. What confused me was, when I viewed movie.pdb file generated by the following command, gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n index.ndx -o movie.pdb two hydrogen molecules of my organic compound, were unbonded to

Re: [gmx-users] regarding pbc issue

On 1/13/18 7:53 AM, Vidya R wrote: Hi gmx users, I used the following commands after simulation run (organic compound in water, to calculate rdf) gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc gmx

[gmx-users] regarding pbc issue

Hi gmx users, I used the following commands after simulation run (organic compound in water, to calculate rdf) gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc gmx trjconv -pbc mol -center -s PRD.tpr -f