Re: [gmx-users] Print Neighbour list

[Paolo Conflitti]

Thank you for your answer.

Unfortunately, that is exactly what I am trying to do. However, what I 
need is more of a custom neighbour search for specific particle-water 
interactions (i.e. one atom against all the neighbour water molecules), 
than a completely new class. And I need to do it at runtime, since I 
will use this information as input for other operations.

However, I think I got the gist of it, thanks to your previous answer.

Again, thanks for everything.

Best,
Paolo

Il 28/01/2019 14:03, Mark Abraham ha scritto:

Hi,

gmx select does this kind of operation already, if what you want to do is
not part of the simulation... It is implemented by its own simple but
fairly efficient search. The neighbor search code is intended for
consumption by the short-range kernels, and you do not want to get involved
with that unless you have to!

Mark

On Mon, 28 Jan 2019 at 12:49 Paolo Conflitti 
wrote:


Thanks for your prompt reply.

I wanted to print the neighbour list to better understand the way it is
processed.
I am currently trying to modify the Gromacs code in order to print only
the neighbour list of the water molecules around a certain atom. I got
inside the code and I found the algorithms that process this kind of
information, but I also wanted to see how the data are organized.
May I ask you if you know of a different way or variable (maybe a
commented line somewhere inside Gromacs) that will allow me to do
something similar?

Best,
Paolo

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Re: [gmx-users] Print Neighbour list

[Mark Abraham]

Hi,

gmx select does this kind of operation already, if what you want to do is
not part of the simulation... It is implemented by its own simple but
fairly efficient search. The neighbor search code is intended for
consumption by the short-range kernels, and you do not want to get involved
with that unless you have to!

Mark

On Mon, 28 Jan 2019 at 12:49 Paolo Conflitti 
wrote:

> Thanks for your prompt reply.
>
> I wanted to print the neighbour list to better understand the way it is
> processed.
> I am currently trying to modify the Gromacs code in order to print only
> the neighbour list of the water molecules around a certain atom. I got
> inside the code and I found the algorithms that process this kind of
> information, but I also wanted to see how the data are organized.
> May I ask you if you know of a different way or variable (maybe a
> commented line somewhere inside Gromacs) that will allow me to do
> something similar?
>
> Best,
> Paolo
>
> --
> Gromacs Users mailing list
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] Print Neighbour list

[Paolo Conflitti]

Thanks for your prompt reply.

I wanted to print the neighbour list to better understand the way it is 
processed.
I am currently trying to modify the Gromacs code in order to print only 
the neighbour list of the water molecules around a certain atom. I got 
inside the code and I found the algorithms that process this kind of 
information, but I also wanted to see how the data are organized.
May I ask you if you know of a different way or variable (maybe a 
commented line somewhere inside Gromacs) that will allow me to do 
something similar?


Best,
Paolo

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Re: [gmx-users] Print Neighbour list

[Mark Abraham]

Hi,

That's only supported by the group scheme, which is not the default in
2018.3. Probably the output would only be useful from a single-rank run,
because the searching might be done and reported in terms of indices of
atoms local to the domain being searched, rather than global.

Mark

On Mon, 28 Jan 2019 at 11:50 Paolo Conflitti 
wrote:

> Dear Gromacs community,
>
> I am trying to print the neighbour list of my simulations.
> Following the manual, I added the GMX_DUMP_NL environment variable in my
> .profile bash file (export GMX_DUMP_LN=1). However, I cannot see any
> neighbour list printed in my .log file. I am sure that the env variable
> is properly read, since it appears inside the .log file. I am currently
> using Gromacs 2018.3.
>
> Thank you in advance for any help you may give me.
>
> Best,
> Paolo
>
>
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[gmx-users] Print Neighbour list

[Paolo Conflitti]

Dear Gromacs community,

I am trying to print the neighbour list of my simulations.
Following the manual, I added the GMX_DUMP_NL environment variable in my 
.profile bash file (export GMX_DUMP_LN=1). However, I cannot see any 
neighbour list printed in my .log file. I am sure that the env variable 
is properly read, since it appears inside the .log file. I am currently 
using Gromacs 2018.3.


Thank you in advance for any help you may give me.

Best,
Paolo


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Re: [gmx-users] Print neighbour list

[Mark Abraham]

Hi,

In the code, it wants you to set GMX_DUMP_NL > 0. And please do everyone a
favour and use a version of GROMACS that isn't  over five years out of its
supported lifetime :-)

Mark

On Sat, Feb 17, 2018 at 12:07 AM fabio trovato 
wrote:

> Hi,
>
> I am trying to output the neighbor list calculated during a simulation. I
> consulted the manual which says that DUMPNL is the env variable suited for
> this purpose.
>
> In my bash script I first set up:
> export DUMPNL=10
>
> and then run the simulation (GROMACS version 4.5.4).
>
> I do not see any neighbor list printed in my md.log file. What am I doing
> wrong? Does anyone knows how to solve this?
>
> Thank you,
> Fabio
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[gmx-users] Print neighbour list

[fabio trovato]

Hi,

I am trying to output the neighbor list calculated during a simulation. I
consulted the manual which says that DUMPNL is the env variable suited for
this purpose.

In my bash script I first set up:
export DUMPNL=10

and then run the simulation (GROMACS version 4.5.4).

I do not see any neighbor list printed in my md.log file. What am I doing
wrong? Does anyone knows how to solve this?

Thank you,
Fabio
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