[gmx-users] g_msd

[Kay Gottschalk]

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?
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