[gmx-users] a snapshot of NVT

Hi, all When I run a small peptide at NVT stage, I get a snapshot like this: I am not sure if it right, and can I use it for NPT ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.co

Re: [gmx-users] a snapshot of NVT

Hi Maggin, Okay, this image may require a bit of explanation :p VMD has drawn bonds according to the bondedness in a reference file. But the atoms have moved, and some went over the box boundaries. So they show up with long bonds crossing the whole box. It's not a problem, just a visualization art

[gmx-users] a snapshot of NVT

Hi, all When I run a small peptide at NVT stage, I get a snapshot like this: I am not sure if it right, and can I use it for NPT ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.co