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ngmx
- nivedita
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10 years 11 months ago #1576
by nivedita
ngmx was created by nivedita
Hi all,
when i check the molecule motion via using the command ngmx -f traj.xtc -s md.tpr -n index.ndx and i select "BB".
I observe that molecule is coming out of the box is it problematic?
i have to repeat all steps with increase box size or is it OK ?
Note :only few residue are coming out
Thanks in advance
when i check the molecule motion via using the command ngmx -f traj.xtc -s md.tpr -n index.ndx and i select "BB".
I observe that molecule is coming out of the box is it problematic?
i have to repeat all steps with increase box size or is it OK ?
Note :only few residue are coming out
Thanks in advance
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- xavier
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10 years 11 months ago #1581
by xavier
Replied by xavier on topic ngmx
The molecule moving out of the box is a consequence of the periodic boundary conditions ... check the gromacs manual for more info about this or google it :))
nivedita wrote: Hi all,
when i check the molecule motion via using the command ngmx -f traj.xtc -s md.tpr -n index.ndx and i select "BB".
I observe that molecule is coming out of the box is it problematic?
i have to repeat all steps with increase box size or is it OK ?
Note :only few residue are coming out
Thanks in advance
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10 years 11 months ago #1588
by nivedita
Replied by nivedita on topic ngmx
hi Xavier,
I already extract trajectory by trjconv -f md.xtc -s md.tpr -o traj.xtc -pbc nojump after that i used following command ngmx -f traj.xtc -s md.tpr -n index.ndx for visualizing the molecule motion, few molecule is moving out off the box.
my question is that i repeat simulation with increase box size or is it ok ?
Thanks in advance
I already extract trajectory by trjconv -f md.xtc -s md.tpr -o traj.xtc -pbc nojump after that i used following command ngmx -f traj.xtc -s md.tpr -n index.ndx for visualizing the molecule motion, few molecule is moving out off the box.
my question is that i repeat simulation with increase box size or is it ok ?
Thanks in advance
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10 years 11 months ago #1589
by xavier
Replied by xavier on topic ngmx
Your question suggests that you have not completely captured the concept of periodic boundary conditions. It is meant to allow molecules to get out of the box and get back in through another face of the box.
using trjconv -pbc no jump mean the trajectory will let molecules follow their "real" path in space without counting that they come back in the box. So their movement away from the original box is fine and should not be considered a reason to increase the box size.
A box size should allow at least 1.0 nm and up to 1.4 nm from the solute (placed at the center of the box) to the box edges.
using trjconv -pbc no jump mean the trajectory will let molecules follow their "real" path in space without counting that they come back in the box. So their movement away from the original box is fine and should not be considered a reason to increase the box size.
A box size should allow at least 1.0 nm and up to 1.4 nm from the solute (placed at the center of the box) to the box edges.
nivedita wrote: hi Xavier,
I already extract trajectory by trjconv -f md.xtc -s md.tpr -o traj.xtc -pbc nojump after that i used following command ngmx -f traj.xtc -s md.tpr -n index.ndx for visualizing the molecule motion, few molecule is moving out off the box.
my question is that i repeat simulation with increase box size or is it ok ?
Thanks in advance
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