Poor scaling with MPI on many-core machines can also be due uneven job
distributions across cores or jobs being wastefully swapped between cores. You
might be able to fix this with some esoteric configuration options of mpirun
(--bind-to-core worked for me with openMPI), but the surest option is
Hi,
I'm seeing MD simulation running a lot slower with the sd integrator than with
md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no documented
indication that this should be the case.
Timings and logs pasted in below - wall time seems to be accumulating up in
Update and Rest, add
These symptoms sound a lot like a bug I reported back in 2010:
http://redmine.gromacs.org/issues/433 - closed with only a short comment from
Berk that it was fixed for 4.5. With my fix as detailed in the redmine report
I've been happily doing NPT replica exchange with my custom code forked from
Hi,
I'm not clear on the meaning and implications of this warning message from
grompp:
WARNING 1 [file ../md.mdp]:
With coulomb soft core, the reciprocal space calculation will not
necessarily cancel. It may be necessary to decrease the reciprocal space
energy, and increase the cutoff ra
Hi David and Berk,
I guess the best proper solution would be to use a Parrinello-Rahman barostat.
>But in Gromacs this is currently not implemented in a reversible way.
>
> Yes, I would love to see a barostat that samples the correct distribution.
Can you clarify? The wording in the manual impl
> The question is:
> Do you trust you simulations when you/others do not find significant problems
> or do you only trust your simulations when you are sure the integrators etc
> are implemented exactly correctly or at least the magnitude of the (small)
> errors are known.
>
> Personally I (and th
Hi Fabricio,
It's not correct to change your value of alpha, you should use a single value
for the whole transformation. The soft core potential is constructed so that
the end points at lambda=0 and 1 represent the 'native' states (with no
influence from the soft core parameters), and that inte
> So what you mean is that I should either use soft core for
> the entire transformation or not use it at all. But then I do not
> understand what Carsten said about using at least on lambda values
> close to 0 and 1. I thought that if I used soft core on the last point
> of my transformation (the
Hello,
The gromacs manual states that for cubic spline interpolation of potential
energy and forces, "V and V’ are continuous, while V” is the first discontinuous
derivative." This makes sense to me as there is a unique solution for
parameters
A2 and A3 if V and V' to the left and right are giv
ouldn't it make more
sense for trjconv to write out the last frame?
Thanks,
Floris
- Forwarded Message
From: Floris Buelens
To: gmx-users@gromacs.org
Sent: Mon, 4 October, 2010 11:24:57
Subject: last frame in trr
Hi,
I want to write out only the final frames from a set of trr tra
Hi,
I want to write out only the final frames from a set of trr trajectories. This
was discussed here:
however intuitively it seems trjconv should do this with the -dump option
documented like this:
-dumptime -1 Dump frame nearest specified time (ps)
if I give e.g. -dump 99
The biotin-streptavidin interaction is on the order of -75 kJ/mol, so a binding
free energy of -300 kJ/mol (dissociation constant of 10^-52 M) means something
is fundamentally wrong - start by taking a hard look at your protocol, as
convergence problems wouldn't account for that kind of deviatio
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