[gmx-users] non-symmetric matrix and too large first values
medeawan at sohu.com
medeawan at sohu.com
Fri May 16 05:52:01 CEST 2003
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
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