[gmx-users] A question on electron density.
leehk at umich.edu
Tue Oct 26 18:51:02 CEST 2004
I'm trying to analyze electron density profiles.
What I did was that....
1) I modified electrons.dat file like below.
For water and ions,
2) I recreated **.tpr file with modified .itp and .top file. (because
different atom types have same atom names). When I executed grompp to
recreate tpr file, it read new .itp file and .top file, neglecting .gro
3) I did "g_density -f **.xtc -s **.tpr -ei electrons.dat -ed -o
**.xvg -sl 200"
The problem is that when I used unmodified electrons.dat (OW=8, HW1=1,
HW2=1), the electron density of water layer was reasonable (338 e/nm3),
compared with experimental result. But, when I used modified
electrons.dat (OW=8.82, HW1=0.59, HW2=0.59), the electron density of
water layer has ~270 e/nm3, which is much less than reasonable result.
I think they both should have same value because they both have total
value 10 (=ow+hw1+hw2).
Could you tell me how to solve this problem? Have you done electro
density analysis like this way??
Thanks for your help in advance.
More information about the gromacs.org_gmx-users