[gmx-users] MSD

[Roman Holomb]

Dear colleagues,

Thanks for reply!

Maybe I'm doing something wrong with using g_msd .....

I have computed MD (5ns) for system containing 100 anion and 100 cation 
molecules.
Results of ACFs, RDFs look good but not MSD....

So I have 2_emi_BF4_100.tpr, 2_emi_BF4_100.trr, 2_indexEMI.ndx files. 
Index file contained numbers of EMI-cation molecules.

Then I use command:
g_msd -f 2_emi_BF4_100.trr -n 2_indexEMI.ndx -s 2_emi_BF4_100.tpr -o 
2_emi_BF4_100_msd_EMI_full.xvg -mol 2_emi_BF4_100_msd_full_D_EMI.xvg

And I have resulted Diffusion constants fitted from 0 to 5000 (ps) 
D[EMI]=(0.002+/-0.003)*10-5 cm2/s
The resulted MSD graph is included.

Then I try to use time 0-20 ps for fitting:

g_msd -f 2_emi_BF4_100.trr -n 2_indexEMI.ndx -s 2_emi_BF4_100.tpr 
-beginfit 0 -endfit 20 -o 2_emi_BF4_100_msd_EMI_0_20.xvg -mol 
2_emi_BF4_100_msd_0_20_D_EMI.xvg

The resulted D: 0 to 20 (ps) D[EMI]=(0.508+/-0.253)*10-5 cm2/s. But MSD 
graphs look ideally the same.....

I'm not sure that program read number of molecules (instead of atoms). 
option -mol give only D for different molecules but not their average 
MSD....
Also -trestart option dosn't work and give me "Segmentation Fault".......

Any comments are advisable.

Thanks in advance!

Sincerely
/Roman
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