[gmx-users] A question on electron density.

Hwankyu Lee leehk at umich.edu
Tue Oct 26 18:51:02 CEST 2004

Dear gromacs-users,

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.


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