[gmx-users] pbc atom

Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Aug 24 17:57:54 CEST 2010


The box dimensions that I type at the bottom of the .gro file are
0.00000 0.00000 0.00000

In regards to the other points you made I'll get back to you as soon as
I can

Many Thanks

chris.neale at utoronto.ca wrote:
> Yup, just got the link. Thank you for posting, and sorry that I missed
> it. It seems possible that Justin is correct and you'll get good data
> if you take it out of the pullx.xvg file (perhaps the g_dist tool is
> wrapping pbc for you).
> 1. How big is your box definition in your .gro file?
> You are right that you need the actual distance, which is not provided
> directly. I think you want this (assuming that cols 5,6,7 give you the
> dx,dy,dz, which I believe that they do):
> cat pullx.xvg | grep -v '[#|@]' | awk '{print
> $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data
> 2. If you do this to a window > 2.0 nm and generate a histogram, do
> you still get two peaks?
> A quick look at the src/tools/gmx_dist.c file indicates that it should
> only apply periodicity if you give it a .tpr where PBC was applied --
> you can check this by comparing the dx, dy, dz out of g_dist with the
> values in pullx.xvg
> If the problem is not solved here, then you can send me off-list all
> the files needed to run a window around 2.5 nm plus all the output
> that you have obtained from a single run and I'll take a look if you
> wish. If you'd rather not do that and there are still problems, then
> perhaps you can post a step by step from the beginning where you copy
> and paste absolutely all of your commands (e.g. paste the *exact*
> grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and
> the last line in your starting .gro file.
> Chris.
> -- original message --
> [gmx-users] pbc atom
> Gavin Melaugh gmelaugh01 at qub.ac.uk
> Tue Aug 24 17:19:45 CEST 2010
>     * Previous message: [gmx-users] pbc atom
>     * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
> Hi Chris
> Yeah I posted the histograms a few days ago as Justin said. Did you get
> the link?
> Gavin
> chris.neale at utoronto.ca wrote:
>> I have seen this before, and there are a few possible reasons, but I'm
>> still waiting to see that histogram with two peaks
>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>> It's really hard to help you when we have to guess what the problem
>> looks like... or perhaps you posted it and I missed it?
>> -- original message --
>> O.K thanks anyway
>> Justin A. Lemkul
>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>> Gavin Melaugh wrote:
>>>> Thanks Justin
>>>> Have you any idea why when generating umbrella histograms for the
>>>> pmf I
>>>> would get two peaks in the histograms above a distance of 2 nm, but
>>>> below 2 nm I get well behaved histograms that lead to a very
>>>> good profile in the pmf. To the best of my knowledge the
>>>> configurations
>>>> are all very well equilibrated at their respective COM distances.
>>>> Umbrella sampling is performed on all windows using a force
>>>> constant of
>>>> 1000 kj/mol at 600 K.

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