[gmx-users] spliting trajectory g_hbond -contact

Mark Abraham mark.j.abraham at gmail.com
Sun Feb 9 02:37:27 CET 2014


No idea, but take a small trajectory, cut it in half, and see!

On Feb 8, 2014 11:37 AM, "Kavyashree M" <hmkvsri at gmail.com> wrote:

> Dear users,
> I need a small clarification . I have to get an index file for the
> contact between protein and water with a cut of distance of
> 0.35 nm. its a 20ns run. When i use g_hbond along with -contact
> it runs for a while, say few ns and gets killed due to the memory
> overload. The system I use has 16Gb RAM and i cannot increase it.
> So the question is instead of calculating the contact between the
> two entities for the whole trajectory, if I split the trajectory into 2
> halves and then calculate the contact, will the combined index
> file obtained be same as the one had I used the whole trajectory?
> Thank you
> regards
> Kavya
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