[gmx-users] pbc atom

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Aug 24 17:40:25 CEST 2010

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.


-- original message --

[gmx-users] pbc atom
Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Aug 24 17:19:45 CEST 2010

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Hi Chris

Yeah I posted the histograms a few days ago as Justin said. Did you get
the link?

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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