Re: [gmx-users] Freezing structure's atom

[Hadi Rahmaninejad]

Hello Mateusz,

First of all, I don’t know where should I use these these commands, should I 
use for instance in equilibration input file like nvt. mdp file? Second, in 
which file I should include ndx file? Could you please provide me an example?

Thank you,
Hadi

Sent from my iPhone

> On Mar 20, 2019, at 4:07 PM, Mateusz Bieniek  wrote:
> 
> Hi Hadi,
> 
> To freeze atoms you have to first create the right group in your index file
> .ndx. Then, you use this:
> 
> freezegrps   = slab
> freezedim= Y Y N
> 
> Where the Ys refer to X Y Z, meaning here the slab group is frozen in X Y
> dimension but not Z dimension.
> 
> Please not that the pressure calculation breaks down when freezing atoms.
> In that case, they should be excluded from the pressure calculation -
> however this has not been implemented for a couple of years now in Verlet
> algorithm.
> 
> For reference:
> http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-freezegrps
> 
> 
> On Wed, 20 Mar 2019 at 15:55, Hadi Rahmaninejad 
> wrote:
> 
>> Hello dear Gromacs users,
>> 
>> I know how to restrain atoms of an structure solvated in water with force
>> with option "-DPOSRES". However, for my simulation, I need to exclude
>> position changing from the simulation, in other words, I need to exactly
>> fixed them. I highly appreciate if any of you can help me with this.
>> 
>> Thank you in advance,
>> Hadi
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at
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>> posting!
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>> 
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[gmx-users] NTMPI / NTOMP combination: 10 threads not "reasonable" for GROMACS?

[Stéphane Téletchéa]

Dear all,

I am wondering why i am getting this error message while launching 
GROMACS (2016.6 for instance):


"NOTE: Your choice of number of MPI ranks and amount of resources 
results in using 10 OpenMP
threads per rank, which is most likely inefficient. The optimum is 
usually between 2 and 6 threads per rank."


The node I am trying to compute on is:



Running on 1 node with total 20 cores, 40 logical cores, 2 compatible GPUs
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: AVX2_256

  Hardware topology: Basic
  GPU info:
    Number of GPUs detected: 2
    #0: NVIDIA Tesla P100-PCIE-12GB, compute cap.: 6.0, ECC: yes, stat: 
compatible
    #1: NVIDIA Tesla P100-PCIE-12GB, compute cap.: 6.0, ECC: yes, stat: 
compatible




Those CPUs are 10 cores +HT (so not 4 or 6). Is it only a warning.

I have tried to launch mdrun using -ntmpi 4 (1 per CPU, 1 per GPU) 
-ntomp 10 but I'm not really

"sure" of what should be used in this situation.

Any clarification / precision appreciated (and I am aware of Best Bang 
for your bucks if that matters :-).


Best,

Stéphane

--
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UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes 
cedex 03, France
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Re: [gmx-users] Freezing structure's atom

[Mateusz Bieniek]

Hi Hadi,

To freeze atoms you have to first create the right group in your index file
.ndx. Then, you use this:

freezegrps   = slab
freezedim= Y Y N

Where the Ys refer to X Y Z, meaning here the slab group is frozen in X Y
dimension but not Z dimension.

Please not that the pressure calculation breaks down when freezing atoms.
In that case, they should be excluded from the pressure calculation -
however this has not been implemented for a couple of years now in Verlet
algorithm.

For reference:
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-freezegrps


On Wed, 20 Mar 2019 at 15:55, Hadi Rahmaninejad 
wrote:

> Hello dear Gromacs users,
>
> I know how to restrain atoms of an structure solvated in water with force
> with option "-DPOSRES". However, for my simulation, I need to exclude
> position changing from the simulation, in other words, I need to exactly
> fixed them. I highly appreciate if any of you can help me with this.
>
> Thank you in advance,
> Hadi
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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[gmx-users] NPT step after energy minimization

[Jianna Blocchi]

Dear all
The box simulation contains polymer and ions.I should perform the energy 
minimization followed by NPT step.I use Parrinello-Rahman barostat. 
continuation=nogen-vel=yesgen-temp=300But when I perform NPT step, I get an 
error:
WARNING 1 [file npt.mdp]:  You are generating velocities so I am assuming you 
are equilibrating a  system. You are using Parrinello-Rahman pressure coupling, 
but this can  be unstable for equilibration. If your system crashes, try 
equilibrating  first with Berendsen pressure coupling. If you are not 
equilibrating the  system, you can probably ignore this warning.
Any suggestions are appreciated.
Thank you.

With Best Regards.


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[gmx-users] Freezing structure's atom

[Hadi Rahmaninejad]

Hello dear Gromacs users,

I know how to restrain atoms of an structure solvated in water with force
with option "-DPOSRES". However, for my simulation, I need to exclude
position changing from the simulation, in other words, I need to exactly
fixed them. I highly appreciate if any of you can help me with this.

Thank you in advance,
Hadi
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[gmx-users] Different models of TMAO

[Dilip.H.N]

Hello all,
I have run a simulation with TMAO using Charmm36 FF and i want to see
whether different models of TMAO ie., Kast, Netz and Garcia models do
solvate/behave in the same way.
So, can anybody share the relevant parameter files as .rtp, .itp etc., of
the above mentioned three different TMAO models required to run the
simulations...
 How can i include the epsilon and LJ parameters in it...?

Any suggestions are appreciated.
Thank you.
---
With Best Regards,

Dilip.H.N
Ph.D. Student.

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[gmx-users] gpu cpu use

[Mario Andres Rodriguez Pineda]

Hi everybody
I have acces to one computer with 2 GPU and 2 CPU. Can i use both GPU and
both CPU in a simulation?
Each cCPU have 10 cores and 20 threads
I'm trying whith this command:
mpirun -np 4 gmx mdrun -ntomp 6 -gpu_id 00
but i don't undesrtand these numbers and i can use it

Thanks for your help .

-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
*Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091
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Re: [gmx-users] Vanishing cofactors

[Erik Marklund]

Hm. Issue largely resolved itself. The chain labels disappear with 2019.1, 
which is why I might have misinterpreted the output pdb. Still an issue, but 
minor. Redmine issue updated.

Kind regards,
Erik

> On 20 Mar 2019, at 14:45, Erik Marklund  wrote:
> 
> Sorry. Wrong link. Here is the correct one
> http://redmine.gromacs.org/issues/2900
> __
> Erik Marklund, PhD, Associate Professor  of Biochemistry
> Associate Senior Lecturer in Computational Biochemistry
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4562
> erik.markl...@kemi.uu.se
> 
> On 20 Mar 2019, at 14:41, Erik Marklund 
> mailto:erik.markl...@kemi.uu.se>> wrote:
> 
> Dear dynamicists,
> 
> When I use a pdb file coming directly from pdb2gmx as input for editconf, my 
> protein’s two cofactor vanish mysteriously. This is using 2019.1. With 2016.3 
> I get no such issues. Is this a known issue? Has anyone experienced similar 
> problems?
> 
> I could not fine anything similar in redline, so I created an issue
> http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1
> 
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Associate Professor  of Biochemistry
> Associate Senior Lecturer in Computational Biochemistry
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4562
> erik.markl...@kemi.uu.se
> 
> 
> 
> 
> 
> 
> 
> 
> 
> När du har kontakt med oss på Uppsala universitet med e-post så innebär det 
> att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan 
> du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
> 
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Re: [gmx-users] Vanishing cofactors

[Erik Marklund]

Sorry. Wrong link. Here is the correct one
http://redmine.gromacs.org/issues/2900
__
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se

On 20 Mar 2019, at 14:41, Erik Marklund 
mailto:erik.markl...@kemi.uu.se>> wrote:

Dear dynamicists,

When I use a pdb file coming directly from pdb2gmx as input for editconf, my 
protein’s two cofactor vanish mysteriously. This is using 2019.1. With 2016.3 I 
get no such issues. Is this a known issue? Has anyone experienced similar 
problems?

I could not fine anything similar in redline, so I created an issue
http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se









När du har kontakt med oss på Uppsala universitet med e-post så innebär det att 
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[gmx-users] Vanishing cofactors

[Erik Marklund]

Dear dynamicists,

When I use a pdb file coming directly from pdb2gmx as input for editconf, my 
protein’s two cofactor vanish mysteriously. This is using 2019.1. With 2016.3 I 
get no such issues. Is this a known issue? Has anyone experienced similar 
problems?

I could not fine anything similar in redline, so I created an issue
http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se









När du har kontakt med oss på Uppsala universitet med e-post så innebär det att 
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du 
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

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[gmx-users] Central atom for improper dihedral

[Tam, Benjamin]

Dear gromacs user,

For the improper dihedral function type 4, when writing in [ dihedraltypes ], 
which position in the naming is the central atoms? Thank you very much.

Best regards,

Ben
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