kay.gottschalk at weizmann.ac.il
Fri Jun 27 12:59:00 CEST 2003
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?
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
>> 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
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
More information about the gromacs.org_gmx-users