Arun kumar wrote:
Dear gmx-users,
I want to discuss and understand about an
error I am getting only at times.... I am simulating a DPPC double
bilayer phase(got the coordinates from Dr Tieleman's website). I used
genbox -cs to get double bilayer. Then i started simulations
normally.
When I use g_density -b 500 I get the following error
*** glibc detected *** free(): invalid next size (normal):
0x0000000000713260 *** Aborted
It is giving a empty density.xvg file
I get same error if I use g_density -b 1000
I checked the reproducibility of the error...... I am getting it
always(I mean I am using g_density once again again,,,,, Not
simulating the system once again again)
But when I use g_density -b 1500 or more I am getting densities
normally.....
Actually i am doing simulations at 4 different temperatures..... But
I am getting the error only for three temperatures.... For one
temperature Every thing is fine......
Gromacs version I am using is : 3.3.1
I checked the archives and in google.... I found a similar error in
archives for make_ndx
After checking in google I came to know that its a common bug with
glibc package of different versions..... Now i want to know is there
anything wrong in my simulations(possibilities) and also how I can rid
of these errors.........
You stand a much better chance of getting a response if you make your
requests easy to read. That means using conventional English
punctuation, ie. not ending most sentences with an ellipsis. Your use of
ellipses in the above text makes it read like it is a stream of
consciousness that you haven't thought through clearly. That makes
people not want to do your work - thinking clearly about your problem
and describing it well - and thus never getting around to giving you any
insight.
I have never used g_density, but I had look at the man page for 30
seconds and I can think of two reasons why doing an analysis starting at
point c would work when it doesn't work starting at a or b, when a<b<c.
Since it only happens for one of your 4 near-identical simulations, this
suggests one of my reasons isn't right... and so I think there is a
problem with your output between b and c for the one that breaks. Go and
look at the log file and see what went wrong.
I didn't apply much knowledge here, I just thought about the problem
clearly. Perhaps this would have occurred to you if you'd thought about
things this way before posting :-)
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
