t the opposite
or something else?
Thank you
Alb
Messaggio originale
Da: albita...@virgilio.it
Data: 3-dic-2009 12.44 PM
A:
Ogg: [gmx-users] g_densmap and xpm files
Hi all.
I have a question about xpm files produced by g_densmap.
I would like, if possible, to extract informati
Hi all.
I have a question about xpm files produced by g_densmap.
I would like, if possible, to extract information in numerical format, such as
for example a single txt file with three columns 'x y density' for all the
points on the grid chosen.
These should be the information which are contained
quite critical to be modeled?
Thank you for your help.
Alb
Messaggio originale
Da: x.peri...@rug.nl
Data: 19-ott-2009 2.04 PM
A: "albita...@virgilio.it", "Discussion list for GROMACS
users"
Ogg: Re: [gmx-users] time steps and segmentation fault
The type of syste
Hi all,
I carried out a MD simulation using the MARTINI CG force field and I had some
problems. The simulation stops immediately, reporting a segmentation fault:
**+
Making 1D domain decomposition 2 x 1 x 1
starting mdrun 'FIB'
20 steps, 6000.0
inable crashes are,
when the output clearly tells you what the problem is.
I am very sorry to say so, but I will not help you any more on this topic.
Anyhow I think the problem should be solved now.
Berk
Date: Thu, 8 Oct 2009 15:58:41 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Sub
ll depend on the second derivative of
the potential.
Berk
Date: Thu, 8 Oct 2009 11:01:39 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential -
Problem
Hi,
I used gmxcheck and gxmdump to compare the results o
thanks,
AM
Messaggio originale
Da: mark.abra...@anu.edu.au
Data: 5-ott-2009 11.19 PM
A: "Discussion list for GROMACS users"
Ogg: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem
albita...@virgilio.it wrote:
> Hi,
> I came back to my original stretch
bra...@anu.edu.au
Data: 5-ott-2009 11.19 PM
A: "Discussion list for GROMACS users"
Ogg: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem
albita...@virgilio.it wrote:
> Hi,
> I came back to my original stretching potential in tabulated form and I
> have
eed. grompp simply assumes dx is the last x divided by n-1.
For Gromacs 4.1 I have put a check in grompp.
If two consecutive delta x's differ by more than 1% you get a fatal error
and you can not proceed.
Berk
Date: Fri, 2 Oct 2009 16:09:55 +0200
From: albita...@virgilio.it
To: gmx-users@gr
ra (intermediate, smoothed) points
or use a small amount of points. But in the end they should be equally spaced
for computational efficiency.
mdrun could, in principle, also do this job, but it is better if the user
thinks about this.
Berk
Date: Thu, 1 Oct 2009 17:13:30 +0200
From: albita...@virg
I assume you have done this, as I have built a check in grompp to give
a warning when the potential and the force are inconsistent.
Berk
Date: Thu, 1 Oct 2009 08:53:51 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: RE: R: Re: R:[gmx-users] Tabulated potential- Pro
d potential
- Problem
-->
Hi,
Are you really sure you entered the tabulated potential correctly?
There is for instance the pre-factor 1/2 in front of the harmonic potential,
which you will have to add explicitly, either in the table or in the force
constant.
Berk
Date: Wed, 30 Sep
t for GROMACS users"
Ogg: Re: R: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem
albita...@virgilio.it wrote:
> I changed bond type to 8.
> In any case the two MD simulations (same harmonic potential but in
> analytical form vs tabulated form) gives different
m type 9 to 8 will generate the exclusions.
Berk
Date: Tue, 29 Sep 2009 17:52:03 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem
In my simulation I used bond type 9 because I was convinced that 1-2 LJ
interacti
abulated bond type 8 and 9
is that 8 does generate exclusions and 9 does not.
Berk
Date: Tue, 29 Sep 2009 14:17:37 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: RE: R: RE: [gmx-users] Tabulated potential - Problem
Hi,
in order to check further which kind of problems are
4:10:08 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: RE: [gmx-users] Tabulated potential - Problem
Unfortunately, my box sizes are not close to 23. I also carried out
calculations switching off PBC or on much smaller systems.
I received always the same error.
I tri
Berk
Date: Fri, 25 Sep 2009 14:10:08 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: R: RE: [gmx-users] Tabulated potential - Problem
Unfortunately, my box sizes are not close to 23. I also carried out
calculations switching off PBC or on much smaller systems.
I receiv
is says.
The distance between two atoms is more than 10 times as large as your table
length.
Maybe you are somehow having issues with periodic boundary conditions.
Is you box size close to 23?
Berk
Date: Thu, 24 Sep 2009 12:32:36 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subjec
Hi,
I'm trying to carry out a CG simulation and I'm using
a tabulated potential for a bond stretching term.
My MD simulations stops immediately with the error message:
---
Program mdrun_mpi, VERSION 4.0.5
Source code file: bondfree.c, line: 1772
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