[gmx-users] Re: Chain separation problem

[Mark Abraham]

> Dear Periole,
> Thank you so much for your kind reply, as you suggested I will keep the
> discussion on the users list. Please note that I AM GETTING PROBLEM ONLY
> WHEN I AM NOT USING ANY BOX.

Please also refrain from using all-capitals. It is regarded as the email
equivalent of shouting. It will get your email ignored, rather than
treated with more urgency.

If your proteins-are-moving apart problem is not a PBC artifact, and does
not occur when you use PBC, then you have a perplexing problem. First,
check your inputs again, so that you really are doing what you think
you're doing. Even repeat the whole setup from scratch. The simplest
explanation is user error.

Mark