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
<<attachment: MSDs_EMI.JPG>>
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