Re: [gmx-users] gmx make_ndx: select last created group without knowing its number

[Peter Kroon]

Or, alternatively, use gmx select with the -sf and -on flags.


Peter


On 22-01-17 13:57, Mark Abraham wrote:
> Hi,
>
> Sure, you can give and refer to groups either by name or number, so there
> are many possible solutions for you. Easiest is to give it a name at the
> time you make it, and then use that name later. Otherwise, you could delete
> all the other groups so that the group you want is always group 1.
>
> Mark
>
> On Sun, Jan 22, 2017 at 1:51 PM CLARK NICOLAS Joan 
> wrote:
>
>> Dear gmx users,
>>
>>
>> I want to check how big are the biasing forces of a collective variable
>> compared to the normal MD forces. As my collective variable only takes into
>> account certain atoms of the system, I'd like to use make_ndx to create a
>> group containing these atoms and give a name to that group so that I can
>> use it later in a script
>>
>>
>> The problem is that I am running this calculation for a lot of systems,
>> some of them with ligands, some of them without, so I would like to use a
>> script to create these groups for all my systems.
>>
>>
>> As the number of the last created group will not always be the same, I was
>> wondering if there is any option in make_ndx that allows to select the last
>> group on the list so i can give it a suitable name without knowing its
>> group number.
>>
>>
>> Thanks,
>>
>> Joan
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] gmx make_ndx: select last created group without knowing its number

[Mark Abraham]

Hi,

Sure, you can give and refer to groups either by name or number, so there
are many possible solutions for you. Easiest is to give it a name at the
time you make it, and then use that name later. Otherwise, you could delete
all the other groups so that the group you want is always group 1.

Mark

On Sun, Jan 22, 2017 at 1:51 PM CLARK NICOLAS Joan 
wrote:

> Dear gmx users,
>
>
> I want to check how big are the biasing forces of a collective variable
> compared to the normal MD forces. As my collective variable only takes into
> account certain atoms of the system, I'd like to use make_ndx to create a
> group containing these atoms and give a name to that group so that I can
> use it later in a script
>
>
> The problem is that I am running this calculation for a lot of systems,
> some of them with ligands, some of them without, so I would like to use a
> script to create these groups for all my systems.
>
>
> As the number of the last created group will not always be the same, I was
> wondering if there is any option in make_ndx that allows to select the last
> group on the list so i can give it a suitable name without knowing its
> group number.
>
>
> Thanks,
>
> Joan
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] gmx make_ndx: select last created group without knowing its number

[CLARK NICOLAS Joan]

Dear gmx users,


I want to check how big are the biasing forces of a collective variable 
compared to the normal MD forces. As my collective variable only takes into 
account certain atoms of the system, I'd like to use make_ndx to create a group 
containing these atoms and give a name to that group so that I can use it later 
in a script


The problem is that I am running this calculation for a lot of systems, some of 
them with ligands, some of them without, so I would like to use a script to 
create these groups for all my systems.


As the number of the last created group will not always be the same, I was 
wondering if there is any option in make_ndx that allows to select the last 
group on the list so i can give it a suitable name without knowing its group 
number.


Thanks,

Joan
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.