[gmx-users] MSD and merging trajectory files

Lars Poulsen lpoulsen at chem.au.dk
Thu Jan 17 14:40:35 CET 2002

Thanks David!

I don't know how I missed trjcat!

I've been looking at the other tool for calculating MSD, g_analyze. From the appearance of the output, this program uses multiple time origins for calculating MSD?
However, I have some problems understanding the output. An example:
I use a coord. input file (.xvg made with g_traj) from a 39.78 ns simulation. g_analyze informs me correctly:  
  Read 30 sets of 3978 points, dt = 10
But then it says:
  1989,  time =19890
And the output file only contains the MSD from t=0 to t=19890ps
What happened to the other half of the data points?

mvh Lars

> On Wed, 16 Jan 2002, Lars Poulsen wrote:
> >Hi!
> >Since I'm not an expert at C code I was wondering, if anyone on the list 
> >could enlighten me about the MSD routine in GROMACS: g_msd.
> >I looks to me like g_msd is calculating <|r(t)-r(0)|>^2 averaged over 
> >the molecules/atoms in the given group - which is all fine. However, it 
> >seems to operate with only one time origin (t=0), which is not so fine 
> >when you want to improve statistics. (from the output: the 'noise level' 
> >is constant over time and it has sharp jumps)  Is this observation 
> >correct?
> >Is there a flag for g_msd I have overlooked? Or should I use g_analyse 
> >instead? Or somethingelse?
> This is a common misunderstanding. Using multiple origins (by splitting up 
> the trajectory) does not give you any improved statistics. You just add up 
> the numbers in different order. The best way to extract diffusion 
> constants is to take the slope of the MSD, after disregarding the first 
> few ps. You can however split the trajectory in bits, and calculate 
> diffusion from that. This may enable you to make an error estimate if the 
> pieces of trajectory are sufficiently independent. It will however not 
> change the average D.
>  >Because of some instabilities in my linux system, I had to restart my 
> >md-simulation several times using tpbconv. Initially, I thought mdrun 
> >would then continue writing in the same trajectory files as before, but 
> >this appears not to be the case. So now I have several traj. files, that 
> >I would like to merge into one. Is there an utility for that in GROMACS?
> trjcat
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  75123 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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