Berk Hess wrote:
> Hi,
>
> That I have thought about and it would avoid a lot of trouble.
> But I have not done that, because that would lead to different run results
> every time you rerun grompp, which can be misleading when you are
> trying to assess the effects of other parameters.
>
> But mayb
important than the second?
Berk
Date: Thu, 5 Feb 2009 10:43:22 +0100
From: r.fried...@bioc.uzh.ch
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] micelle disaggregated in serial, but not parallel,
runs using sd integrator
Hi,
Maybe it's a good idea to have ld-seed=-1
Hi,
Maybe it's a good idea to have ld-seed=-1 as a default if that's not
already the case.
Ran.
Berk Hess wrote:
> Hi,
>
> I don't know why I did not add checks for ld-seed before.
> Now grompp gives a note when continutation=yes and ld-seed!=-1.
>
> tpbconv will now generate a new ld-seed when re
Hi,
I don't know why I did not add checks for ld-seed before.
Now grompp gives a note when continutation=yes and ld-seed!=-1.
tpbconv will now generate a new ld-seed when reading a trajectory
(but you should not use tpbconv, use a checkpoint file instead).
But yesterday I forgot to tell that th
Hi,
In this manner you use the same random seed and thus noise for all parts.
In most cases this will not lead to serious artifacts with SD,
but you can never be sure.
When checkpoints are used, you do not repeat random numbers.
This also gives a difference between serial and parallel in 4.0.
Wit
Hi,
SD will tau_t=0.1 will make your dynamics a lot slower.
I don't see a reason why there should be a difference between serial and
parallel.
Are all simulations single runs, or do you do restarts?
Did you compare the temperatures to check if there is no strong energy loss
or heating and if t
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