[gmx-users] non-symmetric matrix and too large first values

[medeawan at sohu.com]

Thanks for your answer Bert and David:

I have checked the first eigenvalues in .xvg files, some of them really large.
For example, a 88 amino acid protein (PDB ID=1krn), there are 79 amino 
acid coordinates in the PDB file. After EM, the Max force< 1e-9, while the
first 12 eigenvalues g_nmeig_d worked out are:
     1     0.000438558
     2    -0.000683771
     3     -0.00292664
     4      0.00597364
     5      0.00817211
     6      -0.0114438 
     7         1.58334
     8         1.80916
     9         2.04356
    10          2.6188
    11         2.87512
    12         3.44095

For DNA, some results are also strange. As I said in my last mail,
I added lines to the .hdb:
DADE    1
        2       3       N6      C6      N1
DCYT    1
        2       3       N4      C4      N3
DGUA    2
        1       1       N1      C2      C6
        2       3       N2      C2      N1
DTHY    1
        1       1       N3      C2      C4

And in order to join single nucleic acid together, I changed some atom
names in the DNA part of the .rtp file: 
+N --> +P
-C --> -C3*
O3* --> -O3*

Since when I use the command "grompp_d -f em.mdp -c 2iii.gro -p 2iii.top -o 
in.tpr -po in.mdp", there should be a warning message:
 "WARNING 1 [file "2iii.top", line 2508]:
  No default Proper Dih. types, using zeroes"
I add gd_9 or gd_11 to the first dihedral line, so that line can be:
"   2     1     4     5     1    gd_11" 
or
"   2     1     4     5     1    gd_9".
(It's a -OA-P- dihedral)

I have no idea which dihedral number is more reasonable, so I used all the
3 types to compare -- the eigenvalues really have big differents:

For a 2 nucleic acid A-A, the first 12 eigenvalues are:
	          0	       gd_9	     gd_11
1	-2.2617e-08	-8.46442e-08	1.38749e-07
2	 4.3653e-08	  6.6471e-07	2.12549e-07
3         -6.05105e-08	-1.46967e-06	-8.11187e-07
4	4.71581e-07	 -0.00446328	-0.00125328
5         -1.81963e-06	   0.0324086	0.00445241
6	3.72382e-06	  -0.0363397	-0.00489594
7	2.04559	          3.84028	           5.16989
8	3.20175	          10.0408	           7.00483
9	10.1923	          11.6979	           13.4114
10	11.8547	          17.5464	           20.7567
11	20.6515	          22.0428	           29.7425
12	43.1207	          52.4134	           36.5532

For a 20 nucleic acid CTCAA-GGTGT-CCCAG-CCCAC, the first 12 eigenvalues are:
	         0	                  gd_9	    gd_11
1	3.73088e-05	-2.59139e-05	 9.76281e-06
2	-0.000153511	3.50443e-05	-1.34763e-05
3	0.000574301	-0.000357439	 0.00030759
4	-0.00113997	0.000468474	-0.000441709
5	-0.0285976	            0.00105487	 0.000877102
6	0.0324488	           -0.00142717	-0.00124924
7	0.184117	             0.0829609	0.64291
8	0.297109	             0.166827 	0.908421
9	0.617796	             0.39677   	1.78765
10	0.68352	             0.809834	           1.92865
11	1.37551	             1.12581           	2.39546
12	1.67154	             1.24509	           2.93631

I wonder if there is something wrong in my process, and why there are so
big differents between the three group of eigenvalues when a ended dihedral
type changed.

Thanks for any help.
                                          Sincerely yours
                                          Medeawan