[gmx-users] Different RMSD of the same system

[Dechang Li]

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
=========================================