Thanks a bunch for the help Mark!
I made some additional changes that seem to work the way I need it.
src/mdlib/sim_util.c:122: fprintf(stderr, "Fraction complete: %g\n",
(step - ir->init_step) / (float) ir->nsteps);
src/mdlib/sim_util.c-123-
src/mdlib/sim_util.c-124- f = fopen("progress
Jack Shultz wrote:
I am hoping for an update every 10 minutes just to satisfy the anxieties
of volunteers crunching on my project, but every hour may be
satisfactory. And if I can do this without requiring any shell scripts
it would be better in my environment. So I started making some code
mo
Ah of course!
fc = (int)dt / ir->nstlist;
I should cast these as data types that support decimals right?
On Thu, Sep 24, 2009 at 6:44 PM, Jack Shultz
wrote:
> I am hoping for an update every 10 minutes just to satisfy the anxieties of
> volunteers crunching on my project, but every hour may be
I am hoping for an update every 10 minutes just to satisfy the anxieties of
volunteers crunching on my project, but every hour may be satisfactory. And
if I can do this without requiring any shell scripts it would be better in
my environment. So I started making some code modifications which appare
Jack Shultz wrote:
I figured out another way to update the progress of my simulation, but I
need to report the fraction of completion at the certain intervals of
mdrun. Possibly at every time step or if that does not make sense every
100 timesteps. I don't think this is a feature currently supp
varsha gautham wrote:
Dear gmx user,
Am a beginner to gromacs,I have a few questions to be clarified before
getting started with gromacs.
You probably want to start by reading a textbook (or the gromacs manual)
and some review papers.
1.on giving pdb2gmx gromacs offers force fields fom
Varsha: have you subscribed to the list yet? Please do so if you
haven't.
On Sun, 2009-03-22 at 13:18 +0400, varsha gautham wrote:
> 3. hen how to choose a timestep for a simulation like a picosecond or
> a nanosecond?What is a timestep?
>
> I have gone through many materials and stuffs related t
On Sun, Mar 22, 2009 at 2:52 PM, varsha gautham
wrote:
> Dear gmx user,
>
>
> Am a beginner to gromacs,I have a few questions to be clarified before
> getting started with gromacs.
>
> 1.on giving pdb2gmx gromacs offers force fields fom 0 to 6 and also i
> read like opls-aa is the best forcefield
Thank a lot to all for your inputs..
Ramya.
> Hi,
>
> In principle Gromacs should never just crash with a segmentation
> fault, but at least give you a (perhaps cryptic) error message and
> exit somewhat gracefully.
>
> As far as I know there is only one exception to this: If you are
> using ta
Ramya,
A timestep of dt=0.002 already means a timestep of 2fs, since the unit
of dt is ps. So a timestep of dt=0.002=2 fs works fine for you, which is
perfectly normal. If you want to go higher you need to use certain
tricks, as suggested by Xavier.
I suggest you read the manual (e.g.
http://www.
Hi,
In principle Gromacs should never just crash with a segmentation
fault, but at least give you a (perhaps cryptic) error message and
exit somewhat gracefully.
As far as I know there is only one exception to this: If you are
using tabulated interactions the table can only be of finite s
It is not possible to answer your question from the information you give.
A lot of things can cause a segmentation fault. From compilation to
your particular system. Put a search on the user-list, you'll get an idea
of possible problems.
It depends what you will be looking at but I would suggest
10 ns of a solvated protein of regular size should not require much
computing time.
Increasing the time-step above 2 fs is a solution to increase the
speed of the run but then you face the problem of not integrating
the fast movement correctly and this can end up in large forces
and then you run
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