Roman Holomb wrote:
Dear colleagues,
Thanks for reply!
Maybe I'm doing something wrong with using g_msd .....
no your system is freezing.
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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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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