[gmx-users] Different RMSD of the same system

[Tsjerk Wassenaar]

Hi Dechang Li,

If your simulations are different, the results will be different. It's chaos!

Cheers,

Tsjerk

2009/7/13 Dechang Li <li.dc06 at gmail.com>:
> Dear all,
>
>        I have did a simulation with explict water model using Gromacs-3.3.3.
> To save the hard disk space, I didn't collect the coordinates of water by
> using the following parameters:
>
> dt                     = 0.002 ; ps !
> nsteps                 = 30000000 ; total time.
> nstcomm                = 1
> nstxout                = 30000000 ;
> nstenergy              = 1000
> nstvout                = 30000000
> nstlog                 = 20000
> nstxtcout              = 1000
> xtc_grps               = Protein
>
>
>        In addition, I did a short simulation of the system in which the
> coordinates of water were collected every 2 ps. For comparison, I calculated
> the RMSD of C-alpha atoms of the protein. However, the values are
> different of the two systems!  Are these differences reasonable?
>
>        BTW: I didn't generate the velocities in the beginning.
>
>
> RMSD of C-alpha atoms without collecting water coordinates:
> @ subtitle "C-alpha after lsq fit to C-alpha"
>   0.0000000    0.0001220
>   2.0000000    0.0545500
>   4.0000000    0.0691709
>   6.0000005    0.0657938
>   8.0000000    0.0723884
>  10.0000000    0.0800556
>  12.0000010    0.0745629
>  14.0000010    0.0732903
>  16.0000000    0.0752474
>  18.0000000    0.0774800
>  20.0000000    0.0914096
>  22.0000019    0.0981914
>  24.0000019    0.0983810
>  26.0000019    0.1057151
>  28.0000019    0.1053288
>  30.0000019    0.1084988
>
>
> RMSD of C-alpha atoms with collecting water coordinates:
> @ subtitle "C-alpha after lsq fit to C-alpha"
>   0.0000000    0.0002658
>   2.0000000    0.0569104
>   4.0000000    0.0642647
>   6.0000005    0.0673439
>   8.0000000    0.0760661
>  10.0000000    0.0837568
>  12.0000010    0.0978260
>  14.0000010    0.1037093
>  16.0000000    0.1087546
>  18.0000000    0.1126641
>  20.0000000    0.1321630
>  22.0000019    0.1270466
>  24.0000019    0.1102782
>  26.0000019    0.1115073
>  28.0000019    0.1304575
>  30.0000019    0.1173159
>
>
>
> Best regards,
>
>
>
> =========================================
> Dechang Li, Ph.D Candidate
> Department of Engineering Mechanics
> Tsinghua University
> Beijing 100084
> P.R. China
>
> Tel:   +86-10-62773574(O)
> Email: lidc02 at mails.tsinghua.edu.cn
> =========================================
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623