[gmx-users] MSD

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Thu Apr 13 10:24:15 CEST 2006


I think I agree with David.... 100 cations and 100 anions without 
solvent (am I correct?)... probably your system is freezing and an 
evidence of this is that the slope of your MSD graph tends to zero, so 
your D tends to zero too.

But considering what you said about ACFs and RDFs, I think you know what 
you are doing and I´ll talk about only MSD.

Your MSD plot is right for me. It starts with a non-linear part and 
after (near 1.5 ns) it become reasonable linear. But I think you need 
more statistic and I suggest you run more 5 ns of simulation the get a 
better linear part.

The differences between values of D calculated with and without fitting 
is that in the first case you are fitting the Einstein equation (see 
manual) in hole graph. In the second case you are using times 0-20 and 
fitting the equation only in this part of the graph and, like you can 
see on it, the curve have a high slope in the beginning. Actually, you 
should use the begin-endfit option from 1.5 ns until the end of graph to 
fit the Einstein equation only to the "linear" part.

About -trestart, it works restarting the initial position of the 
molecule every X ps. Try to use 1, 5 and 10 ps values for it and see 
what happen.

Well... summarizing... try to run more 5 ns of simulation, run msd using 
-beginfit from the begin of linear part of your graph, play with 
t_restart values.

I hope I helped you.


Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - São Carlos - Brasil

Roman Holomb wrote:

> 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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