[gmx-users] g_msd

[David]

On Fri, 2003-06-27 at 12:58, Kay Gottschalk wrote:
> Thanks! I did use such an index file.  But when I iuse the combination  
> -trestart -mol, I always get this 'bus error' when I reach the ps  
> specified with -trestart. I am actually considering taking the bus home  
> now. Individually the two options work fine.
> Unrelated question: in your descriptions you often have this nice  
> cryptic writing ' t MOD dt ='. What really does it mean? t modulo dt?
yes, is this cryptic? Quite normal mathematics I would think...


> Thanks,
> Kay.
> 
> On Friday, June 27, 2003, at 01:01 PM, David wrote:
> 
> > On Fri, 2003-06-27 at 11:50, Kay Gottschalk wrote:
> >> Hi there,
> >>
> >> I want to calculate the mean square displacement for each individual  
> >> of
> >> my water molecules in steps of 2 ps - would something like g_msd -mol
> >> -trestart 2 do that?? That would mean, that I get 250 different
> >> displacements for a 500 ps simulation, if I am not mistaken (at least
> >> that's what I want). Or does it average all these 250 different
> >> displacements? What is also kind of unfortunate is that I get a 'bus
> >> error' when I do  'g_msd -f full -s full -mol -trestart 2'. Why might
> >> that be? I'm afraid I don't really understand what I am doing with
> >> g_msd and which options I have...
> >
> > a little detail is that g_msd expects "molecule" numbers in the index
> > file with the -mol flag, so for your average 216 spc box, you'd have
> > numbers 1 through 216
> >
> >>
> >> _______________________________________________
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> > --  
> > Groeten, David.
> > _______________________________________________________________________ 
> > _
> > Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> > 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://xray.bmc.uu.se/~spoel
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> > +
> > _______________________________________________
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> >
> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
> Tel: ++972-8-9343639
> Herzl St. 1
> Rehovot 76100
> Israel
> 
> _______________________________________________
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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