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ngmx
- nivedita
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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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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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- nivedita
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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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- xavier
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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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