On 9/14/2007 5:35 PM, [EMAIL PROTECTED] wrote:
Selon Yang Ye <[EMAIL PROTECTED]>:
Deshuffling shall be made before 2), 3) and 4).
Furthermore, be aware that if you use the 'sort' option, you'll also need to
desort ...
IIRC, there is a g_desort program that does all in one (it was published on the
list some time ago), and should be avaialbe in next gromacs version.
Stéphane
Instead, -shuffle and -sort will all disappear in the next version. I
encourage Frankie to benchmark the speed-up ratio, especially it is not
a membrane system. I know that people would not use -sort/shuffle so as
not to mess things up for some "little" lost in speed. That's just alright.
On 9/14/2007 11:36 AM, Frankie Montenegro wrote:
Hi guys,
A stupid question: I got myself confused with this
shuffling/deshuffling thing, which I
shouldn't have been doing with protein in the first place. So this
are my steps, done
on the same 4 nodes, please tell me whether I was supposed to do any
deshuffling
of .trr and .gro files, and following which steps:
1)minimization, supplied output .gro to the next step
2)equilibration, supplied output .gro to the next step
3) NVT run, supplied output .gro and .trr to the next step
4) NPT run
A simple YES or NO for each step will suffice.
Thanks,
Frankie
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