[gmx-users] MSD

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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