[gmx-users] g_RMS

[Michal Kolinski]

Hi all

I used g_rms  to calculate RMSD for peptide ligand (inside receptor active site) for 2 ns simulation.  I don't understand why are the obtained values for RMSD so high (are the units nm, or A)?   From the trajectory it looks like  ligand is very  stable.  

Thank you in advance.

Michal    

 

 

My g_rmsd output:.

#          This      file        was      created by        g_rms_mpi                                                      

#          which   is          part      of         G         R         O         M        A         C         S:

#          Gravel  Rubs    Often   Many   Awfully            Cauterized       Sores                                      

#          All        this       happened         at:        Tue      Oct      25        13:51:37          2005                

#                                                                                                                               

@        title       RMSD                                                                                               

@        xaxis    label     Time (ps)                                                                                           

@        yaxis    label     RMSD (nm)                                                                                       

@TYPE          xy                                                                                                                  

@        subtitle DAM after lsq fit to DAM                                                                                                     

0          0,0002                                                                                                           

2          1,8792                                                                                                           

4          1,3783                                                                                                           

6          1,3538                                                                                                           

8          2,0421                                                                                                           

10        2,0478                                                                                                           

12        2,0536

14        2,4779

16        2,4665

18        3,1466

20        2,642

22        2,6397

24        2,9798

26        4,1681

28        2,9859

30        2,9585

32        3,2852

34        3,2984

36        3,2861

38        4,0952 ...

.

.

..

-- 
Ten list został przeskanowany przez program ArcaMail
Silnik (2005-06-03/2005-10-25)
This message has been scanned by ArcaMail
Engine (2005-06-03/2005-10-25)
http://www.mks.com.pl
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051025/9cb10a8f/attachment.html>