Hi,
I recommend to run the regressiontests. The simplest way is to build
GROMACS with cmake -DREGRESSIONTEST_DOWNLOAD, and run make check.
See
http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_4.12._Testing_GROMACS_for_correctness
for more details.
Roland
On Thu, Jun 6, 2013
On 12/04/2012 3:30 PM, priya thiyagarajan wrote:
hello sir,
Thanks for your kind reply..
i am performing final md run for 60molecules ..
after i submitted my job for 5ns, when i analyse the result my run is
completed only for 314ps initially..
At this point, you should have looked at your .
shivangi nangia wrote:
Hello gmx users,
My system for NVT equilbration runs into segmentation fault as soon as I
try to run it.
It does not give any warning or hint of what might be going wrong.
Since I am a new user I am having difficulty exploring the plausible
reasons.
System: Protein(
Hello gmx users,
My system for NVT equilbration runs into segmentation fault as soon as
I try to run it.
It does not give any warning or hint of what might be going wrong.
Since I am a new user I am having difficulty exploring the plausible
reasons.
System: Protein( polyhistidine), 20 2,5-d
Sikandar Mashayak wrote:
It happens immediately at step 0., and the log file looks like :
That suggests to me that the system is inherently unstable, which can occur for
a variety of reasons.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
A few more comments below.
Input
It happens immediately at step 0., and the log file looks like :
Input Parameters:
integrator = md
nsteps = 2
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_
Sikandar Mashayak wrote:
Hi
I have gromacs input files for md simulation, with these set up files
(*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on
one machine, but when I move it to other machine, I get segmentation
fault when I do mdrun. Both the machines have exactly
sunny mishra wrote:
Dear all,
At the final step of my mdrun I get LINCS warning. I don't know whats
the issue. Please help me out.
If I had a nickel for every time I saw a LINCS warning on this list... :)
The answer is always the same. There is something physically unrealistic about
y
Hi,
Have a look at the coordinates in the PDB file that mdrun is dumping.
You will likely see that a group of atoms (e.g. a sidechain) is
moving violently and/or breaking up completely just before the crash.
There can be plenty of reasons for this. One possibility is that you
have a small number
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