[gmx-users] How to draw a RMSD plot after essential dynamics analysis(EDA)

zhang xudong zxdcs01 at hotmail.com
Sun May 9 16:31:30 CEST 2004

Dear all
       I have just finished a MD simulation about a enzyme using gromacs. 
My aim is to analysis the conformation change of some loops with and 
without the substrate. so,I use essential dynamics analysis(EDA)to process 
the data as follows:
1. I use g_covar program process .xtc and .tpr files in order to build 
covariance matrix and diagonalize it.(only C-alpha atoms are include in the 
matrix).command line as follows:
g_covar -f 1R42_md.xtc -s 1R42_md.tpr -v eigenvec.trr 

2. then use g_anaeig program to get a new trajectory which is calculated 
from the old trajectory(1R42_md.xtc)by applying the most significant 
eigenvectors(I choose the first 8 eigenvectors as gromacs default).command 
line as follows:
g_anaeig -v eigenvec.trr -f 1R42_md.xtc -s 1R42_md.tpr -filt filtered.xtc
3. next, I use g_rmsf program and want to calculate a RMSD for the first 8 
eigenvectors  as a function of alpha carbons. command as follows:
g_rmsf -f filtered.xtc -s 1R42_md.tpr -od rmsdev.xvg

but when i hit the enter, it display a fatal error: Molecule in topology 
has atom numbers below and above natoms (597).You are probably trying to 
use a trajectory which does not match the first 597 atoms of the run input 
file.You can make a matching run input file with tpbconv.

I do not know what happened about it. please give me a detailed 
interpretation because i am a new user og gromacs. I doubt that there are 
fault command line or parametters used above. If they are incorrect, please 
give me a correct ones. My aim is to calculate a RMSD for the first 8 
eigenvectors as a function of alpha carbons. so,you may also tell me the 
procedure on how to draw such RMSD plot useing gromacs modules.

Thanks in advance 

XuDong Zhang
Department of Biology
The University of YunNan,china
zxdcs01 at hotmail.com
zhangxd at ynu.edu.cn

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