nder.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
>
> Hi,
>
> thx for suggesting the workaround, just to make sure I understand the
> workaround correctly:
>
> I devide each slab in 2 sections, one section contains 90% of the atoms
should not produce artifacts.
>
> Berk
>
> > Date: Fri, 2 Oct 2009 10:25:21 +0200
> > From: alexander.h...@mytum.de
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] direction_periodic
> >
> > You did suggest that, but it crashes at step 0
ndering all the time why you are using a potential
> > and not a constraint. I think I had suggested using a constraint some
> > time ago, but I am not sure that I did.
> >
> > Berk
> >
> > > Date: Fri, 2 Oct 2009 09:45:42 +0200
> > > From: alexander
ggested using a constraint some
> time ago, but I am not sure that I did.
>
> Berk
>
> > Date: Fri, 2 Oct 2009 09:45:42 +0200
> > From: alexander.h...@mytum.de
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] direction_periodic
> >
> > Hey,
> >
:42 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
>
> Hey,
>
> I want to pull the diamonds with more or less exactly the speed I give
> for the pulling without the massive noise
> (in gromacs 3.3 this worked
Hey,
I want to pull the diamonds with more or less exactly the speed I give
for the pulling without the massive noise
(in gromacs 3.3 this worked using afm type pulling, after some
equilibration the slabs settled to an almost constant
pull speed without soo much fluctuation using the same paramete
.
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] direction_periodic
Date: Thu, 1 Oct 2009 14:30:57 +0200
Hi,
I ran the initial part of the 0.1 nm/ps simulation again (since I deleted the 1
GB trr file).
I get fluctuating velocities for both groups around
Oct 2009 14:08:28 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
>
> Hi,
>
> did you look at the actual trajectory (trr/xtc) or the velocity of one
> of the diamond slabs (using g_traj) ?
> I do get
continued the simulation long enough.
> > > I'll run it again tomorrow.
> > >
> > > Berk
> > >
> > > > Date: Mon, 28 Sep 2009 16:57:19 +0200
> > > > From: alexander.h...@mytum.de
> > > > To: gmx-users@gromacs.org
> > &g
work fine for me.
>
> Berk
>
> > Date: Thu, 1 Oct 2009 10:24:54 +0200
> > From: alexander.h...@mytum.de
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] direction_periodic
> >
> > Hey,
> >
> > did you find the time to look at it?
expect in a periodic system.
So it seems to work fine for me.
Berk
> Date: Thu, 1 Oct 2009 10:24:54 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
>
> Hey,
>
> did you find the time to look at it?
>
&
> > Strange...
> > > I tested the code on the files you sent me
> > > and the slabs were moving smoothly.
> > >
> > > Berk
> > >
> > > > Date: Mon, 28 Sep 2009 15:40:16 +0200
> > > > From: alexander.h...@mytum.de
> > &
I am not sure I continued the simulation long enough.
I'll run it again tomorrow.
Berk
> Date: Mon, 28 Sep 2009 16:57:19 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
>
> Well..they do move forward for
Sep 2009 15:40:16 +0200
> > From: alexander.h...@mytum.de
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] direction_periodic
> >
> > Hey,
> >
> > so using the new direction_periodic with some kernels that actually work
> > and the sources from th
Strange...
I tested the code on the files you sent me
and the slabs were moving smoothly.
Berk
> Date: Mon, 28 Sep 2009 15:40:16 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
>
> Hey,
>
> so using th
k
>
> > Date: Mon, 21 Sep 2009 16:17:17 +0200
> > From: alexander.h...@mytum.de
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] direction_periodic
> >
> > Hey,
> >
> > ok, I checked this. It works ok with the assembly kernels on my local
&
Hi,
Don't use fortran.
We will get rid of it before the 4.1 release.
Berk
> Date: Mon, 21 Sep 2009 16:17:17 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
>
> Hey,
>
> ok, I checked this. It works
tum.de
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] direction_periodic
> >
> > With master branch you mean the code I get via
> >
> > |git clone git://git.gromacs.org/gromacs.git
> >
> > right?
> >
> > Alex
> > |
> >
&
Yes.
Berk
> Date: Mon, 21 Sep 2009 14:42:43 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
>
> With master branch you mean the code I get via
>
> |git clone git://git.gromacs.org/gromacs.g
With master branch you mean the code I get via
|git clone git://git.gromacs.org/gromacs.git
right?
Alex
|
Berk Hess schrieb:
> I tested on your system and got good results.
> There is still a tricky issue: the pull COM is still determined
> in the "standard" way by summing distances from the
I tested on your system and got good results.
There is still a tricky issue: the pull COM is still determined
in the "standard" way by summing distances from the pbcatom.
Therefore atoms should not change nearest image from he pbcatom.
This would result in nasty noise in the pull COM and force.
I
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