Re: [gmx-users] Distance between the atoms greater than Box length

[Dilip.H.N]

Hi,
I have visualized the molecules in vmd and these two water molecules are
placed diagonally opposite in the box. So, in that case obviously, the
distance will be greater than the box length. And the two water molecules
are within the box only.

And yes, my box here is cubic.

Thank you.



[image: Mailtrack]

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06/05/18,
10:34:06 AM

---
With Best Regards,

Dilip.H.N
PhD Student.

On Tue, Jun 5, 2018 at 7:09 AM, Mark Abraham 
wrote:

> Hi,
>
> Only if the box is cubic.
>
> Mark
>
> On Tue, Jun 5, 2018 at 3:20 AM Quyen V. Vu  wrote:
>
> > Hi Dillip,
> > As Mark suggest, If you want to calculate by your own code, you can put
> the
> > condition to check which is the nearest neighbour by comparing with box
> > length/2
> >
> >
> > On Mon, Jun 4, 2018, 19:42 Mark Abraham 
> wrote:
> >
> > > Hi,
> > >
> > > You have a periodic cell, so in general the distance from A to the
> > nearest
> > > periodic image of B is across a cell boundary. Trjconv cannot produce a
> > > trajectory so that all pairs of A and B will have a non-periodic
> distance
> > > that is the minimum distance. Use a tool that already understands this,
> > > like
> > >
> > >
> > http://manual.gromacs.org/documentation/current/
> onlinehelp/gmx-distance.html
> > > or
> > >
> > http://manual.gromacs.org/documentation/current/
> onlinehelp/gmx-mindist.html
> > > .
> > >
> > > Mark
> > >
> > > On Mon, Jun 4, 2018, 14:01 Dilip.H.N 
> wrote:
> > >
> > > > Hello all,
> > > > I have extracted the trajectory of my system containing all the water
> > > > molecules and my box length is 2.48 ~2.5 nm.
> > > > The command was:
> > > > gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o
> nptmdtrjwater500.gro
> > > -dt
> > > > 60  #i have 6 frames (30ns is the time and saved the
> > coordinates
> > > > for 0.5 ps )and i have extracted a total of 500 frames trajectory
> (-dt
> > 60
> > > > =>3/500).
> > > >
> > > > And i have written a code which calculates the inter-atomic distance
> > (in
> > > my
> > > > case it is inter oxygen distances). And when i calculate it (using
> the
> > > > distance formula ie.,
> > > > {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the
> > oxygen
> > > > atom of say, 7SOL and 6SOL, the distance comes to 3.4520.
> > > >
> > > > Here are the coordinates for two water coordinates as
> representative...
> > > >
> > > > Generated by trjconv : Glycine-Water t=   0.0
> > > > xxx
> > > > .
> > > > .
> > > > .
> > > > 6SOL OW   13   2.405   0.185   1.774
> > > > 6SOLHW1   14   2.452   0.097   1.782
> > > > 6SOLHW2   15   2.466   0.259   1.804
> > > > 7SOL OW   16   0.016   2.177   0.277
> > > > 7SOLHW1   17   0.098   2.141   0.234
> > > > 7SOLHW2   18  -0.064   2.126   0.245
> > > > .
> > > > .
> > > > 2.49238   2.49238   2.49238
> > > >
> > > > How is this possible ie., 3.452 nm, which is greater than the box
> > length
> > > > (2.5 nm). How can the interatomic distance be greater than the box
> > > > length..??
> > > >
> > > > Any suggestions are appreciated.
> > > >
> > > > Thank you.
> > > >
> > > > [image: Mailtrack]
> > > > <
> > > >
> > >
> > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=
> signaturevirality5&
> > > > >
> > > > Sender
> > > > notified by
> > > > Mailtrack
> > > > <
> > > >
> > >
> > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=
> signaturevirality5&
> > > > >
> > > > 06/04/18,
> > > > 5:26:50 PM
> > > >
> > > > ---
> > > > With Best Regards,
> > > >
> > > > Dilip.H.N
> > > > PhD Student.
> > > >
> > > > On Mon, Jun 4, 2018 at 5:15 PM, Dilip.H.N  >
> > > > wrote:
> > > >
> > > > > Hello all,
> > > > > I have extracted the trajectory of my system containing all the
> water
> > > > > molecules and my box length is 2.48 ~2.5 nm.
> > > > >
> > > > > And i have written a code which calculates the inter-atomic
> distance
> > > (in
> > > > > my case it is inter oxygen distances). And when i calculate it
> (using
> > > the
> > > > > distance formula ie.,
> > > > > {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the
> > > oxygen
> > > > > of say
> > > > > 6SOL OW   13   2.405   0.185   1.774
> > > > > 6SOLHW1   14   2.452   0.097   1.782
> > > > > 6SOLHW2   15   2.466   0.259   1.804
> > > > > 7SOL OW   16   0.016   2.177   0.277
> > > > > 7SOLHW1   17   0.098   2.141   0.234
> > > > > 7SOLHW2   18  -0.064   2.126   0.245
> > > > >
> > > > >
> > > > > ---
> > > > > With Best Regards,
> > > > >
> > > > > Dilip.H.N
> > > > > PhD Student.
> > > > > [image: Mailtrack]
> > > > > <
> > > >
> > >
> > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=
> signaturevirality5&
> > > >
> > > 

Re: [gmx-users] Distance between the atoms greater than Box length

[Mark Abraham]

Hi,

Only if the box is cubic.

Mark

On Tue, Jun 5, 2018 at 3:20 AM Quyen V. Vu  wrote:

> Hi Dillip,
> As Mark suggest, If you want to calculate by your own code, you can put the
> condition to check which is the nearest neighbour by comparing with box
> length/2
>
>
> On Mon, Jun 4, 2018, 19:42 Mark Abraham  wrote:
>
> > Hi,
> >
> > You have a periodic cell, so in general the distance from A to the
> nearest
> > periodic image of B is across a cell boundary. Trjconv cannot produce a
> > trajectory so that all pairs of A and B will have a non-periodic distance
> > that is the minimum distance. Use a tool that already understands this,
> > like
> >
> >
> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html
> > or
> >
> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-mindist.html
> > .
> >
> > Mark
> >
> > On Mon, Jun 4, 2018, 14:01 Dilip.H.N  wrote:
> >
> > > Hello all,
> > > I have extracted the trajectory of my system containing all the water
> > > molecules and my box length is 2.48 ~2.5 nm.
> > > The command was:
> > > gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrjwater500.gro
> > -dt
> > > 60  #i have 6 frames (30ns is the time and saved the
> coordinates
> > > for 0.5 ps )and i have extracted a total of 500 frames trajectory (-dt
> 60
> > > =>3/500).
> > >
> > > And i have written a code which calculates the inter-atomic distance
> (in
> > my
> > > case it is inter oxygen distances). And when i calculate it (using the
> > > distance formula ie.,
> > > {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the
> oxygen
> > > atom of say, 7SOL and 6SOL, the distance comes to 3.4520.
> > >
> > > Here are the coordinates for two water coordinates as representative...
> > >
> > > Generated by trjconv : Glycine-Water t=   0.0
> > > xxx
> > > .
> > > .
> > > .
> > > 6SOL OW   13   2.405   0.185   1.774
> > > 6SOLHW1   14   2.452   0.097   1.782
> > > 6SOLHW2   15   2.466   0.259   1.804
> > > 7SOL OW   16   0.016   2.177   0.277
> > > 7SOLHW1   17   0.098   2.141   0.234
> > > 7SOLHW2   18  -0.064   2.126   0.245
> > > .
> > > .
> > > 2.49238   2.49238   2.49238
> > >
> > > How is this possible ie., 3.452 nm, which is greater than the box
> length
> > > (2.5 nm). How can the interatomic distance be greater than the box
> > > length..??
> > >
> > > Any suggestions are appreciated.
> > >
> > > Thank you.
> > >
> > > [image: Mailtrack]
> > > <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> > > >
> > > Sender
> > > notified by
> > > Mailtrack
> > > <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> > > >
> > > 06/04/18,
> > > 5:26:50 PM
> > >
> > > ---
> > > With Best Regards,
> > >
> > > Dilip.H.N
> > > PhD Student.
> > >
> > > On Mon, Jun 4, 2018 at 5:15 PM, Dilip.H.N 
> > > wrote:
> > >
> > > > Hello all,
> > > > I have extracted the trajectory of my system containing all the water
> > > > molecules and my box length is 2.48 ~2.5 nm.
> > > >
> > > > And i have written a code which calculates the inter-atomic distance
> > (in
> > > > my case it is inter oxygen distances). And when i calculate it (using
> > the
> > > > distance formula ie.,
> > > > {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the
> > oxygen
> > > > of say
> > > > 6SOL OW   13   2.405   0.185   1.774
> > > > 6SOLHW1   14   2.452   0.097   1.782
> > > > 6SOLHW2   15   2.466   0.259   1.804
> > > > 7SOL OW   16   0.016   2.177   0.277
> > > > 7SOLHW1   17   0.098   2.141   0.234
> > > > 7SOLHW2   18  -0.064   2.126   0.245
> > > >
> > > >
> > > > ---
> > > > With Best Regards,
> > > >
> > > > Dilip.H.N
> > > > PhD Student.
> > > > [image: Mailtrack]
> > > > <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> > >
> > > Sender
> > > > notified by
> > > > Mailtrack
> > > > <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> > >
> > > 06/04/18,
> > > > 5:15:08 PM
> > > >
> > > --
> > > 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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Re: [gmx-users] Distance between the atoms greater than Box length

[Quyen V. Vu]

Hi Dillip,
As Mark suggest, If you want to calculate by your own code, you can put the
condition to check which is the nearest neighbour by comparing with box
length/2


On Mon, Jun 4, 2018, 19:42 Mark Abraham  wrote:

> Hi,
>
> You have a periodic cell, so in general the distance from A to the nearest
> periodic image of B is across a cell boundary. Trjconv cannot produce a
> trajectory so that all pairs of A and B will have a non-periodic distance
> that is the minimum distance. Use a tool that already understands this,
> like
>
> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html
> or
> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-mindist.html
> .
>
> Mark
>
> On Mon, Jun 4, 2018, 14:01 Dilip.H.N  wrote:
>
> > Hello all,
> > I have extracted the trajectory of my system containing all the water
> > molecules and my box length is 2.48 ~2.5 nm.
> > The command was:
> > gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrjwater500.gro
> -dt
> > 60  #i have 6 frames (30ns is the time and saved the coordinates
> > for 0.5 ps )and i have extracted a total of 500 frames trajectory (-dt 60
> > =>3/500).
> >
> > And i have written a code which calculates the inter-atomic distance (in
> my
> > case it is inter oxygen distances). And when i calculate it (using the
> > distance formula ie.,
> > {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
> > atom of say, 7SOL and 6SOL, the distance comes to 3.4520.
> >
> > Here are the coordinates for two water coordinates as representative...
> >
> > Generated by trjconv : Glycine-Water t=   0.0
> > xxx
> > .
> > .
> > .
> > 6SOL OW   13   2.405   0.185   1.774
> > 6SOLHW1   14   2.452   0.097   1.782
> > 6SOLHW2   15   2.466   0.259   1.804
> > 7SOL OW   16   0.016   2.177   0.277
> > 7SOLHW1   17   0.098   2.141   0.234
> > 7SOLHW2   18  -0.064   2.126   0.245
> > .
> > .
> > 2.49238   2.49238   2.49238
> >
> > How is this possible ie., 3.452 nm, which is greater than the box length
> > (2.5 nm). How can the interatomic distance be greater than the box
> > length..??
> >
> > Any suggestions are appreciated.
> >
> > Thank you.
> >
> > [image: Mailtrack]
> > <
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> > >
> > Sender
> > notified by
> > Mailtrack
> > <
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> > >
> > 06/04/18,
> > 5:26:50 PM
> >
> > ---
> > With Best Regards,
> >
> > Dilip.H.N
> > PhD Student.
> >
> > On Mon, Jun 4, 2018 at 5:15 PM, Dilip.H.N 
> > wrote:
> >
> > > Hello all,
> > > I have extracted the trajectory of my system containing all the water
> > > molecules and my box length is 2.48 ~2.5 nm.
> > >
> > > And i have written a code which calculates the inter-atomic distance
> (in
> > > my case it is inter oxygen distances). And when i calculate it (using
> the
> > > distance formula ie.,
> > > {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the
> oxygen
> > > of say
> > > 6SOL OW   13   2.405   0.185   1.774
> > > 6SOLHW1   14   2.452   0.097   1.782
> > > 6SOLHW2   15   2.466   0.259   1.804
> > > 7SOL OW   16   0.016   2.177   0.277
> > > 7SOLHW1   17   0.098   2.141   0.234
> > > 7SOLHW2   18  -0.064   2.126   0.245
> > >
> > >
> > > ---
> > > With Best Regards,
> > >
> > > Dilip.H.N
> > > PhD Student.
> > > [image: Mailtrack]
> > > <
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> >
> > Sender
> > > notified by
> > > Mailtrack
> > > <
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> >
> > 06/04/18,
> > > 5:15:08 PM
> > >
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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[gmx-users] How can I measure RDC fitness?

[Hanin Omar]

I am including orientation restraints in my md simulation for N-H vectors, how 
can I test RDC fitness to test if my simulation is actually doing what is 
expected of it? 
Thank you for your help
Hanin

Sent from my iPhone
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Re: [gmx-users] gmx 5.1.4, cuda9, Unsupported gpu architecture 'compute_20'

[Tamas Hegedus]

Hi,

I do not do an mdrun -rerun. I think that I can not do it, since I have 
a trajectory with protein only. And I aimed to have a trajectory with 
the protein, water, and ions. Do I misunderstand something?



On 06/04/2018 10:45 PM, Mark Abraham wrote:

Hi,

On Mon, Jun 4, 2018 at 10:40 PM Tamas Hegedus  wrote:


Hi,

I have to rerun a simulation done in gmx 5.1.4 to save also the water
and ions.

First, I took the equilibrated gro and the modified mdp to generate the
input tpr for the production run using gmx 2018.1. The results are
significantly different (I think that this is ok). But I would like to
rerun also with gmx 5.1.4.


I am not aware of a good reason to want to do this, but if you did, you can
use a CPU-only build. gmx mdrun -rerun does not get the full benefit of GPU
offload, anyway.



However, I have to compile the old version and there is cuda9 on the
system I use. I get the nvcc fatal   : Unsupported gpu architecture
'compute_20' error. After running cmake I tried to delete all
-gencode;arch=compute_20,code=sm_20; from the files listed below.
However, they are regenerated after issuing make and make stops with the
same error.

How can I resolve this issue?


GROMACS 5.1.4 supported hardware that CUDA used to support, however the
much more recently released CUDA 9 does not. Either use a newer GROMACS
version, build without CUDA support, or build with an older CUDA version.

Mark



Thanks for your help and suggestion,

Tamas

gromacs-5.1.4/build:

CMakeCache.txt
src/buildinfo.h

src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake

src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_data_mgmt.cu.o.cmake.pre-gen

src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_data_mgmt.cu.o.Release.cmake

src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.cmake.pre-gen

src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gpu_utils/libgromacs_generated_gpu_utils.cu.o.cmake.pre-gen

src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gpu_utils/libgromacs_generated_gpu_utils.cu.o.Release.cmake

src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_pmalloc_cuda.cu.o.Release.cmake

src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_cudautils.cu.o.cmake.pre-gen

src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_pmalloc_cuda.cu.o.cmake.pre-gen

src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o.Release.cmake

src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_cudautils.cu.o.Release.cmake

src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o.cmake.pre-gen


--
Tamas Hegedus, PhD
Senior Research Fellow
MTA-SE Molecular Biophysics Research Group
Hungarian Academy of Sciences  | phone: (36) 1-459 1500/60233
Semmelweis University  | fax:   (36) 1-266 6656
Tuzolto utca 37-47 | mailto:ta...@hegelab.org
Budapest, 1094, Hungary| http://www.hegelab.org

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send a mail to gmx-users-requ...@gromacs.org.



--
Tamas Hegedus, PhD
Senior Research Fellow
MTA-SE Molecular Biophysics Research Group
Hungarian Academy of Sciences  | phone: (36) 1-459 1500/60233
Semmelweis University  | fax:   (36) 1-266 6656
Tuzolto utca 37-47 | mailto:ta...@hegelab.org
Budapest, 1094, Hungary| http://www.hegelab.org

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Re: [gmx-users] gmx 5.1.4, cuda9, Unsupported gpu architecture 'compute_20'

[Mark Abraham]

Hi,

On Mon, Jun 4, 2018 at 10:40 PM Tamas Hegedus  wrote:

> Hi,
>
> I have to rerun a simulation done in gmx 5.1.4 to save also the water
> and ions.
>
> First, I took the equilibrated gro and the modified mdp to generate the
> input tpr for the production run using gmx 2018.1. The results are
> significantly different (I think that this is ok). But I would like to
> rerun also with gmx 5.1.4.
>

I am not aware of a good reason to want to do this, but if you did, you can
use a CPU-only build. gmx mdrun -rerun does not get the full benefit of GPU
offload, anyway.


> However, I have to compile the old version and there is cuda9 on the
> system I use. I get the nvcc fatal   : Unsupported gpu architecture
> 'compute_20' error. After running cmake I tried to delete all
> -gencode;arch=compute_20,code=sm_20; from the files listed below.
> However, they are regenerated after issuing make and make stops with the
> same error.
>
> How can I resolve this issue?
>

GROMACS 5.1.4 supported hardware that CUDA used to support, however the
much more recently released CUDA 9 does not. Either use a newer GROMACS
version, build without CUDA support, or build with an older CUDA version.

Mark


> Thanks for your help and suggestion,
>
> Tamas
>
> gromacs-5.1.4/build:
>
> CMakeCache.txt
> src/buildinfo.h
>
> src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake
>
> src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_data_mgmt.cu.o.cmake.pre-gen
>
> src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_data_mgmt.cu.o.Release.cmake
>
> src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.cmake.pre-gen
>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gpu_utils/libgromacs_generated_gpu_utils.cu.o.cmake.pre-gen
>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gpu_utils/libgromacs_generated_gpu_utils.cu.o.Release.cmake
>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_pmalloc_cuda.cu.o.Release.cmake
>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_cudautils.cu.o.cmake.pre-gen
>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_pmalloc_cuda.cu.o.cmake.pre-gen
>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o.Release.cmake
>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_cudautils.cu.o.Release.cmake
>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o.cmake.pre-gen
>
>
> --
> Tamas Hegedus, PhD
> Senior Research Fellow
> MTA-SE Molecular Biophysics Research Group
> Hungarian Academy of Sciences  | phone: (36) 1-459 1500/60233
> Semmelweis University  | fax:   (36) 1-266 6656
> Tuzolto utca 37-47 | mailto:ta...@hegelab.org
> Budapest, 1094, Hungary| http://www.hegelab.org
>
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> Gromacs Users mailing list
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[gmx-users] gmx 5.1.4, cuda9, Unsupported gpu architecture 'compute_20'

[Tamas Hegedus]

Hi,

I have to rerun a simulation done in gmx 5.1.4 to save also the water 
and ions.


First, I took the equilibrated gro and the modified mdp to generate the 
input tpr for the production run using gmx 2018.1. The results are 
significantly different (I think that this is ok). But I would like to 
rerun also with gmx 5.1.4.


However, I have to compile the old version and there is cuda9 on the 
system I use. I get the nvcc fatal   : Unsupported gpu architecture 
'compute_20' error. After running cmake I tried to delete all 
-gencode;arch=compute_20,code=sm_20; from the files listed below. 
However, they are regenerated after issuing make and make stops with the 
same error.


How can I resolve this issue?

Thanks for your help and suggestion,

Tamas

gromacs-5.1.4/build:

CMakeCache.txt
src/buildinfo.h
src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake
src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_data_mgmt.cu.o.cmake.pre-gen
src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_data_mgmt.cu.o.Release.cmake
src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.cmake.pre-gen
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gpu_utils/libgromacs_generated_gpu_utils.cu.o.cmake.pre-gen
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gpu_utils/libgromacs_generated_gpu_utils.cu.o.Release.cmake
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_pmalloc_cuda.cu.o.Release.cmake
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_cudautils.cu.o.cmake.pre-gen
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_pmalloc_cuda.cu.o.cmake.pre-gen
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o.Release.cmake
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src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o.cmake.pre-gen


--
Tamas Hegedus, PhD
Senior Research Fellow
MTA-SE Molecular Biophysics Research Group
Hungarian Academy of Sciences  | phone: (36) 1-459 1500/60233
Semmelweis University  | fax:   (36) 1-266 6656
Tuzolto utca 37-47 | mailto:ta...@hegelab.org
Budapest, 1094, Hungary| http://www.hegelab.org

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Re: [gmx-users] Box dimension

[rose rahmani]

Is there any suggestion about how can i make this system in least box size?
with periodic boundary condition in all dimensions?put NT in middle or at
z=0?

Best
-Rose

On Mon, Jun 4, 2018 at 2:19 PM, rose rahmani  wrote:

> It's ZnS and yes it's periodic and in water not in vaccum. I used DFT just
> for optimization and obtaining charges.  I did this job for an slab before.
> I mean the AA was between slab surface and wall but it was the vaccum space
> before slab and after wall. imagine this structures in a box of z=12. The
> slab was in z=4 and wall in z=7.5 and WATER between z=4 to7.5  So z=0
> to 4 and 7.5 to 12 is in vaccum. and AA is between z=4 to 7.5 .
> I think it's clear now.
>
> Best regards
> -Rose
>
> On Mon, 4 Jun 2018, 13:37 Alex,  wrote:
>
>> It's a bit unclear what's happening in your system. Are you simulating
>> in vacuum, or in solvent? I am assuming it's in solvent and that the
>> word "vacuum" simply means space unoccupied by the structure, i.e. a
>> term used by DFT folks. With all nanotubes (carbon, ZnS, BN, etc), water
>> forms various interfaces at the boundary, so simply look at the
>> interface data and/or other literature and see roughly how much space is
>> needed to accommodate that in addition to everything else.
>>
>> Yes, people do put their NTs between walls with a periodic boundary,
>> which requires that the nanotube edges are crystallographically
>> periodic, i.e. fits a supercell. It is a very useful practice.
>>
>> Alex
>>
>>
>> On 6/4/2018 2:48 AM, rose rahmani wrote:
>> > Sorry i should correct myself
>> >
>> > On Mon, 4 Jun 2018, 13:10 rose rahmani,  wrote:
>> >
>> >> I have nothing to say...
>> >> but i'm a beginner and i comment here to have your ideas as
>> experienced.
>> >>   It's not CNT. It's an inorganic nanotube which its partial atomic
>> charges
>> >> (0.48 , -0.48) is calculated by DFT.
>> >>
>> >> When i optimized structure in other packages i put it in box with Z=3.
>> So
>> >> first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
>> >> z=2.15 and the "COM" is in z=1.5 .
>> >> So NT outer curvature which is in touch with AA is in z=2.15(0.85 +
>> 1.3)
>> >> Did you calculate these arithmetics when the z dimension of CNT started
>> >> from z=0 to z=1.3?
>> >>
>> >> People sometimes put NT between 2 walls? As the z=7 need much more
>> water
>> >> and long calculations. Do you think put NT between two walls and use
>> vaccum
>> >>
>> > Use box 3times distances between two walls so the vaccum is 2/3 this
>> > distance
>> >
>> >> 3times distances between walls is better
>> >>
>> > than multiply 2 to keep it symmetric?(now you have 1.3 + 2*1.5 +
>> thickness
>> >> of two walls) how do you think, sir?
>> >>
>> >> With regards
>> >> -Rose
>> >>
>> >>
>> >>
>> >>
>> >> On 4 Jun 2018 12:04, "Alex"  wrote:
>> >>
>> >> I'm kind and civil, practically a sweetheart. I just can't put smiley
>> >> faces everywhere! On the other hand, it does not hurt to try things and
>> >> have a little bit of initiative. I don't know why I am telling you
>> this,
>> >> like you've never supervised students... Also, CNTs are simulated
>> >> exactly the same way (within these forcefield flavors) as pretty much
>> >> anything else you can think of. That is, until one day when you guys
>> >> decide to come with a testing Gromacs version that includes FFs not
>> >> relying on permanent topologies. ;)
>> >>
>> >>
>> >> Alex
>> >>
>> >>
>> >>
>> >> On 6/4/2018 1:28 AM, Mark Abraham wrote:
>> >>> Hi,
>> >>>
>> >>> Let's keep the discussion kind and civil, please. What's obvious when
>> you
>> >>> have experience often isn't when you are new. :-) I sure don't
>> understand
>> >>> the arithmetic involved, but then I've never attempted a CNT
>> simulation!
>> >>>
>> >>> Mark
>> >>>
>> >>> On Mon, Jun 4, 2018, 09:08 Alex  wrote:
>> >>>
>>  And again, your question has nothing to do with Gromacs. It has to do
>>  with what you want to do, common sense, and basic arithmetic.
>> 
>>  CNTs interact at pretty short range (if they are intact and without
>> edge
>>  passivation), so I'd just go with a distance sweep range of ~1.5 nm
>> and
>>  give it some additional space, say, 1 nm, and finally keep the box
>>  symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 +
>> 1) x
>>  2 = 7.6 nm. You could of course place the CNT off center (in Z) to
>>  shorten the box.
>> 
>>  Alex
>> 
>> 
>>  On 6/4/2018 12:53 AM, rose rahmani wrote:
>> > Hi,
>> >
>> > I want to do umbrella sampling for different coordination of amino
>> acid
>> > through different distances (in Z dimension) from nanotube. The
>> >> nanotube
>> > axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
>> > curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
>> > (because the nanotube radius is 0.65nm). The initial distance of
>> amino
>>  acid
>> > from nanotube is 2nm. The question is 

Re: [gmx-users] Doubts in visualisation of sdf output

[Justin Lemkul]

On 6/4/18 1:35 PM, Apramita Chand wrote:

Dear Justin,
Thanks for your reply
You're right. I should be choosing a particular density level for all the
components.
There's another doubt. Why Is it necessary to center the protein before
doing g_spatial?


You need a frame of reference for the output to make any sense. You want 
to know the density of given atoms around some solute, so if the solute 
is freely rotating and translating, the output doesn't make sense. If 
it's fit to remove overall global motion, the calculation means something.


-Justin


Thanks

Apramita

On 6/4/18 12:04 PM, Apramita Chand wrote:

Dear Justin,
Thanks for your reply.
I followed your suggestion and generated the output for urea SDF
(gride_urea.cube) and water SDF(grid_water.cube).
When I visualise both together, I get a picture that is attached in the
link as follows:
https://drive.google.com/open?id=1lTF-0pSG4-6p0dQ2W7IQWPiz8CnW5CtO

The isovalue was found to be 30 for grid_urea.cube while isovalue=20 was
found to be more suitable for grid_water.cube.
Is it okay if the isovalues differ?

That depends on what you're doing and what your definition of "suitable"
is. You're choosing two different densities to illustrate different
components. Does that make sense? Are you trying to actually quantify
something or just render an image to show where various things are?

-Justin


Thanking you,
Yours sincerely,
Apramita


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Doubts in visualisation of sdf output

[Apramita Chand]

Dear Justin,
Thanks for your reply
You're right. I should be choosing a particular density level for all the
components.
There's another doubt. Why Is it necessary to center the protein before
doing g_spatial?

Thanks

Apramita

On 6/4/18 12:04 PM, Apramita Chand wrote:
> Dear Justin,
> Thanks for your reply.
> I followed your suggestion and generated the output for urea SDF
> (gride_urea.cube) and water SDF(grid_water.cube).
> When I visualise both together, I get a picture that is attached in the
> link as follows:
> https://drive.google.com/open?id=1lTF-0pSG4-6p0dQ2W7IQWPiz8CnW5CtO
>
> The isovalue was found to be 30 for grid_urea.cube while isovalue=20 was
> found to be more suitable for grid_water.cube.
> Is it okay if the isovalues differ?

That depends on what you're doing and what your definition of "suitable"
is. You're choosing two different densities to illustrate different
components. Does that make sense? Are you trying to actually quantify
something or just render an image to show where various things are?

-Justin

> Thanking you,
> Yours sincerely,
> Apramita
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Re: [gmx-users] Doubts in visualisation of sdf output

[Justin Lemkul]

On 6/4/18 12:04 PM, Apramita Chand wrote:

Dear Justin,
Thanks for your reply.
I followed your suggestion and generated the output for urea SDF
(gride_urea.cube) and water SDF(grid_water.cube).
When I visualise both together, I get a picture that is attached in the
link as follows:
https://drive.google.com/open?id=1lTF-0pSG4-6p0dQ2W7IQWPiz8CnW5CtO

The isovalue was found to be 30 for grid_urea.cube while isovalue=20 was
found to be more suitable for grid_water.cube.
Is it okay if the isovalues differ?


That depends on what you're doing and what your definition of "suitable" 
is. You're choosing two different densities to illustrate different 
components. Does that make sense? Are you trying to actually quantify 
something or just render an image to show where various things are?


-Justin


Thanking you,
Yours sincerely,
Apramita


Message: 6
Date: Mon, 4 Jun 2018 08:03:21 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Doubts in visualisation of sdf output
Message-ID: <06a53787-59cc-ff56-ae75-28a49c2d6...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 6/4/18 7:05 AM, Apramita Chand wrote:

Dear All,
I want the SDF of urea as well as water molecules around my peptide
molecule. For this purpose , I used trjconv to get traj1.xtc with -fit
rot+trans option(selecting peptide as fitting option and system as

output).

Using this traj1.xtc, I generated traj2.xtc with centering the peptide and
again system as output.
On this traj2.xtc, I used g_spatial where I selected Peptide molecule for
SDF and then water molecules to output coordinates.

You want the opposite of that - solvent for SDF and peptide for
coordinate output.

-Justin


The grid.cube files for water and also urea have been formed.
However, how do I visualise the peptide molecule along with the

isosurface?

Should I load a separate file containing only centered peptide

coordinates?

Should that be .gro file for the entire trajectory?

Please advise.

Yours sincerely,
Apramita


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] [SPAM]: Re: Coarse Grained (Empty space In water)

[Justin Lemkul]

On 6/4/18 1:20 PM, Samieegohar, Mohammadreza wrote:

Hi Kevin

The nanoparticle is fixed in the middle of box and is not in the edge.

I used PBC boundary condition

Is it because of water freezing ?


Voids observed during NVT are generally due to setting up an initial box 
that is too large for the given number of particles. NPT equilibration 
should compress the system.


-Justin







From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Kevin Boyd 

Sent: Monday, June 4, 2018 12:58:13 PM
To: gmx-us...@gromacs.org
Subject: [SPAM]: Re: [gmx-users] Coarse Grained (Empty space In water)

Hi,

Why would you want to "ruin" a perfectly good nanoparticle? :)

Could this be a visualization artifact? What kind of treatment of
periodic boundary conditions are you applying prior to visualization?
If you use a PBC option that makes your nanoparticle  contiguous and
not split across periodic boundaries, you would see an empty area in
the box if the nanoparticle is partially out of the box (which would
correspond in size to the fraction of the nanoparticle out of the
box).

Kevin

On Mon, Jun 4, 2018 at 12:48 PM, Samieegohar, Mohammadreza
 wrote:

Hello
I am ruining a nanoparticle inside water. I use coarse grained model for water 
and nanoparticle
My problem is:
When I run the system in NVT 298K , after some steps there is a empty area 
inside the water  (like a hole) while the initial structure has a good 
distribution for water molecules (P4).

May you help me to solve the problem ?

Thanks


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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] [SPAM]: Re: Coarse Grained (Empty space In water)

[Samieegohar, Mohammadreza]

Hi Kevin

The nanoparticle is fixed in the middle of box and is not in the edge.

I used PBC boundary condition

Is it because of water freezing ?






From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Kevin Boyd 

Sent: Monday, June 4, 2018 12:58:13 PM
To: gmx-us...@gromacs.org
Subject: [SPAM]: Re: [gmx-users] Coarse Grained (Empty space In water)

Hi,

Why would you want to "ruin" a perfectly good nanoparticle? :)

Could this be a visualization artifact? What kind of treatment of
periodic boundary conditions are you applying prior to visualization?
If you use a PBC option that makes your nanoparticle  contiguous and
not split across periodic boundaries, you would see an empty area in
the box if the nanoparticle is partially out of the box (which would
correspond in size to the fraction of the nanoparticle out of the
box).

Kevin

On Mon, Jun 4, 2018 at 12:48 PM, Samieegohar, Mohammadreza
 wrote:
> Hello
> I am ruining a nanoparticle inside water. I use coarse grained model for 
> water and nanoparticle
> My problem is:
> When I run the system in NVT 298K , after some steps there is a empty area 
> inside the water  (like a hole) while the initial structure has a good 
> distribution for water molecules (P4).
>
> May you help me to solve the problem ?
>
> Thanks
>
>
> --
> 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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Re: [gmx-users] Coarse Grained (Empty space In water)

[Kevin Boyd]

Hi,

Why would you want to "ruin" a perfectly good nanoparticle? :)

Could this be a visualization artifact? What kind of treatment of
periodic boundary conditions are you applying prior to visualization?
If you use a PBC option that makes your nanoparticle  contiguous and
not split across periodic boundaries, you would see an empty area in
the box if the nanoparticle is partially out of the box (which would
correspond in size to the fraction of the nanoparticle out of the
box).

Kevin

On Mon, Jun 4, 2018 at 12:48 PM, Samieegohar, Mohammadreza
 wrote:
> Hello
> I am ruining a nanoparticle inside water. I use coarse grained model for 
> water and nanoparticle
> My problem is:
> When I run the system in NVT 298K , after some steps there is a empty area 
> inside the water  (like a hole) while the initial structure has a good 
> distribution for water molecules (P4).
>
> May you help me to solve the problem ?
>
> Thanks
>
>
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[gmx-users] Coarse Grained (Empty space In water)

[Samieegohar, Mohammadreza]

Hello
I am ruining a nanoparticle inside water. I use coarse grained model for water 
and nanoparticle
My problem is:
When I run the system in NVT 298K , after some steps there is a empty area 
inside the water  (like a hole) while the initial structure has a good 
distribution for water molecules (P4).

May you help me to solve the problem ?

Thanks


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Re: [gmx-users] Doubts in visualisation of sdf output

[Apramita Chand]

Dear Justin,
Thanks for your reply.
I followed your suggestion and generated the output for urea SDF
(gride_urea.cube) and water SDF(grid_water.cube).
When I visualise both together, I get a picture that is attached in the
link as follows:
https://drive.google.com/open?id=1lTF-0pSG4-6p0dQ2W7IQWPiz8CnW5CtO

The isovalue was found to be 30 for grid_urea.cube while isovalue=20 was
found to be more suitable for grid_water.cube.
Is it okay if the isovalues differ?

Thanking you,
Yours sincerely,
Apramita


Message: 6
Date: Mon, 4 Jun 2018 08:03:21 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Doubts in visualisation of sdf output
Message-ID: <06a53787-59cc-ff56-ae75-28a49c2d6...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 6/4/18 7:05 AM, Apramita Chand wrote:
> Dear All,
> I want the SDF of urea as well as water molecules around my peptide
> molecule. For this purpose , I used trjconv to get traj1.xtc with -fit
> rot+trans option(selecting peptide as fitting option and system as
output).
> Using this traj1.xtc, I generated traj2.xtc with centering the peptide and
> again system as output.
> On this traj2.xtc, I used g_spatial where I selected Peptide molecule for
> SDF and then water molecules to output coordinates.

You want the opposite of that - solvent for SDF and peptide for
coordinate output.

-Justin

> The grid.cube files for water and also urea have been formed.
> However, how do I visualise the peptide molecule along with the
isosurface?
> Should I load a separate file containing only centered peptide
coordinates?
> Should that be .gro file for the entire trajectory?
>
> Please advise.
>
> Yours sincerely,
> Apramita

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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[gmx-users] regarding free energy perturbation

[zhangw]

Dear Gromacs users,
 I am using Gromacs 5.0.6 with CHARMM27 forcefield. I want to do FEP analysis 
and I did it based on this tutorials: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html

. 
But I just want to peturb some atoms of the protein, however, in the mdp file,I 
only can choose whole protein moleculetype.   couple-moltype = Protein
I don’t know how to calculate free energy by only perturbing charge of some 
atoms of protein. 
and I have tried to modify topology file  that I added the state B, liking the 
following: but it seems unable to recognize the state B in topology file.

25  C  3ALA  C 25   0.51 12.011  C  0.00  
12.011 ; qtot 0.465
26  O  3ALA  O 26  -0.51 15.999  O  0.00  
15.999 ; qtot -0.045
; residue   4 ALA rtp ALA  q  0.0
27NH1  4ALA  N 27  -0.47 14.007  NH1 0.00  
14.007 ; qtot -0.515
28  H  4ALA HN 28   0.31  1.008  H  0.00  
1.008 ; qtot -0.205
29CT1  4ALA CA 29   0.07 12.011  CT1 0.00  
12.011 ; qtot -0.135
30 HB  4ALA HA 30   0.09  1.008  HB  0.00  
1.008 ; qtot -0.045
31CT3  4ALA CB 31  -0.27 12.011   ; qtot 
-0.315
32 HA  4ALAHB1 32   0.09  1.008   ; qtot 
-0.225
33 HA  4ALAHB2 33   0.09  1.008   ; qtot 
-0.135
34 HA  4ALAHB3 34   0.09  1.008   ; qtot 
-0.045
35  C  4ALA  C 35   0.51 12.011   ; qtot 
0.465
36  O  4ALA  O 36  -0.51 15.999   ; qtot 
-0.045
; residue   5 ALA rtp ALA  q  0.0
37NH1  5ALA  N 37  -0.47 14.007   ; qtot 
-0.515
38  H  5ALA HN 38   0.31  1.008   ; qtot 
-0.205


but it seems that it can't recognize state B in topology file. And it seems  to 
calculate the free energy just based on the mdp file, couple-moltype = Protein
Mdp file is the following:

; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p    = 1.0
compressibility  = 4.5e-05
ref_p    = 1.0
; Free energy control stuff
free_energy  = yes
init_lambda_state    = 0
delta_lambda = 0
calc_lambda_neighbors    = 1    ; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for 
each simulation
; init_lambda_state    0    1    2    3    4    5    6    7    8    9    10 
  11
vdw_lambdas  = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
coul_lambdas = 0.0 0.01 0.02 0.04 0.06 0.08 0.1 0.15 0.25 0.5 0.75 
1.0
; We are not transforming any bonded or restrained interactions
bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00
restraint_lambdas    = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00
; Masses are not changing (particle identities are the same at lambda = 0 and 
lambda = 1)
mass_lambdas     = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00
; Not doing simulated temperting here
temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00
; Options for the decoupling
sc-alpha = 0.5
sc-coul  = no   ; linear interpolation of Coulomb (none in 
this case)
sc-power = 1.0
sc-sigma = 0.3
couple-moltype   = Protein  ; name of moleculetype to decouple
couple-lambda0   = vdw-q ; only van der Waals interactions
couple-lambda1   = none ; turn off everything, in this case only vdW
couple-intramol  = no
nstdhdl  = 10
; Do not generate velocities
gen_vel  = no
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NPT
continuation = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12


I’m wandering how can I solve the problem ? It would be a great help if anyone 
could help me out here.
Many thanks!

Zhang Xiao 



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Re: [gmx-users] Groove width

[spss4]

 Hii
Thank you for your help. It is working successfully.

Sunipa
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Re: [gmx-users] regarding rmsd calculation

[Justin Lemkul]

On 6/4/18 8:57 AM, SHAHEE ISLAM wrote:

hi,
i am doing thr rmsd calculation of protein,by using the command
gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic.tpr -f
../pbc.xtc/md-0-1.xtc -o rmsd-p1-0-1.xvg -tu ns   (this is for first 1
microsecond)
then again i have done for the next 1 micro second
gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic1.tpr -f
../pbc.xtc/md-1-2.xtc -o rmsd-p1-1-2.xvg -tu ns (i.e from 1 to 2
microsecond)
but the problem is there is no continuity between the last valu of
rmsd-p1-0-1.xvg and last value of rmsd-p1-1-1.xvg

rmsd-p1-0-1.xvg
  0.0000.0049827
0.0200.1721005
0.0400.2209484
0.0600.2384352
.
.
.

999.94006350.8320900
  999.96002200.8242129
  999.98004150.8163539
1000.6100.8269945

and the rmsd-p1-1-1.xvg
0.0000.0049169
0.0200.1181309
0.0400.1274706
0.0600.1289782
.
.
.
999.94006350.5308270
  999.96002200.5303858
  999.98004150.5313085
1000.6100.5300161


The fact that your time values restarted suggests that the simulation 
did not continue from the previous time, rather it restarted from zero 
and you have essentially two separate simulations of 1 microsecond. What 
does visual inspection of the trajectory tell you?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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[gmx-users] regarding rmsd calculation

[SHAHEE ISLAM]

hi,
i am doing thr rmsd calculation of protein,by using the command
gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic.tpr -f
../pbc.xtc/md-0-1.xtc -o rmsd-p1-0-1.xvg -tu ns   (this is for first 1
microsecond)
then again i have done for the next 1 micro second
gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic1.tpr -f
../pbc.xtc/md-1-2.xtc -o rmsd-p1-1-2.xvg -tu ns (i.e from 1 to 2
microsecond)
but the problem is there is no continuity between the last valu of
rmsd-p1-0-1.xvg and last value of rmsd-p1-1-1.xvg

rmsd-p1-0-1.xvg
 0.0000.0049827
   0.0200.1721005
   0.0400.2209484
   0.0600.2384352
.
.
.

999.94006350.8320900
 999.96002200.8242129
 999.98004150.8163539
1000.6100.8269945

and the rmsd-p1-1-1.xvg
0.0000.0049169
   0.0200.1181309
   0.0400.1274706
   0.0600.1289782
.
.
.
999.94006350.5308270
 999.96002200.5303858
 999.98004150.5313085
1000.6100.5300161
 the last value of rmsd-p1-0-1.xvg should almost equal to the first
value of rmsd-p1-1-1.xvg as it is the continuation value starting from
one microsecond. i did not understand why this is happening.
thanking you
shahee
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Re: [gmx-users] Groove width

[rajendra kumar]

On Mon, Jun 4, 2018 at 1:10 PM,  wrote:

> Hii
>> I have tried installation of do_x3dna in ubuntu system following the
>> instructions given in the link. Installation done successfully then I
>> have written the path of do_x3dna in .bashrc file(export
>> do_x3dna=/usr/local/do_x3dna/bin/) and source the file source ~/.bashrc.
>> Then I tried doing do_x3dna -h but it shows do_x3dna not found. What is
>> wrong here? My GROMACS version is 2016.3 . Need suggestion .
>>
>
​You do not have to give -DCMAKE_INSTALL_PREFIX option. Without this
option, do_x3dna will be installed in default directory and It will run
without any additional step.
For questions relating to do_x3dna, please use do_x3dna forum (
https://groups.google.com/forum/#!forum/do_x3dna).
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Re: [gmx-users] Centering the molecule

[Mark Abraham]

Hi,

Trjconv -pbc mol is documented to do a particular thing.

If that's not what you want, even though it may have coincidentally done
what you wanted on some other trajectory, then please reconsider that
choice.

If it's not doing what it says, it would be good to see some more detail
than "it doesn't work how I expected."

Mark

On Mon, Jun 4, 2018, 10:32  wrote:

> Hi all
> I want to center my molecule into a rectangular box by GROMACS. I am using
> the following command:
> gmx trjconv -f  traj.trr -s md.tpr -center -pbc  mol -b 100 -e 120 -o
> test.gro
> But output  shown is still out of the box. This command works for cubic
> box. Is there anything different flag for rectangular box? My box size is
> 5 5 7.
>
> Thanks
> Sunipa
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Re: [gmx-users] Distance between the atoms greater than Box length

[Mark Abraham]

Hi,

You have a periodic cell, so in general the distance from A to the nearest
periodic image of B is across a cell boundary. Trjconv cannot produce a
trajectory so that all pairs of A and B will have a non-periodic distance
that is the minimum distance. Use a tool that already understands this,
like
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html
or
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-mindist.html.

Mark

On Mon, Jun 4, 2018, 14:01 Dilip.H.N  wrote:

> Hello all,
> I have extracted the trajectory of my system containing all the water
> molecules and my box length is 2.48 ~2.5 nm.
> The command was:
> gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrjwater500.gro -dt
> 60  #i have 6 frames (30ns is the time and saved the coordinates
> for 0.5 ps )and i have extracted a total of 500 frames trajectory (-dt 60
> =>3/500).
>
> And i have written a code which calculates the inter-atomic distance (in my
> case it is inter oxygen distances). And when i calculate it (using the
> distance formula ie.,
> {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
> atom of say, 7SOL and 6SOL, the distance comes to 3.4520.
>
> Here are the coordinates for two water coordinates as representative...
>
> Generated by trjconv : Glycine-Water t=   0.0
> xxx
> .
> .
> .
> 6SOL OW   13   2.405   0.185   1.774
> 6SOLHW1   14   2.452   0.097   1.782
> 6SOLHW2   15   2.466   0.259   1.804
> 7SOL OW   16   0.016   2.177   0.277
> 7SOLHW1   17   0.098   2.141   0.234
> 7SOLHW2   18  -0.064   2.126   0.245
> .
> .
> 2.49238   2.49238   2.49238
>
> How is this possible ie., 3.452 nm, which is greater than the box length
> (2.5 nm). How can the interatomic distance be greater than the box
> length..??
>
> Any suggestions are appreciated.
>
> Thank you.
>
> [image: Mailtrack]
> <
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> >
> Sender
> notified by
> Mailtrack
> <
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;
> >
> 06/04/18,
> 5:26:50 PM
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
>
> On Mon, Jun 4, 2018 at 5:15 PM, Dilip.H.N 
> wrote:
>
> > Hello all,
> > I have extracted the trajectory of my system containing all the water
> > molecules and my box length is 2.48 ~2.5 nm.
> >
> > And i have written a code which calculates the inter-atomic distance (in
> > my case it is inter oxygen distances). And when i calculate it (using the
> > distance formula ie.,
> > {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
> > of say
> > 6SOL OW   13   2.405   0.185   1.774
> > 6SOLHW1   14   2.452   0.097   1.782
> > 6SOLHW2   15   2.466   0.259   1.804
> > 7SOL OW   16   0.016   2.177   0.277
> > 7SOLHW1   17   0.098   2.141   0.234
> > 7SOLHW2   18  -0.064   2.126   0.245
> >
> >
> > ---
> > With Best Regards,
> >
> > Dilip.H.N
> > PhD Student.
> > [image: Mailtrack]
> > <
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;>
> Sender
> > notified by
> > Mailtrack
> > <
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;>
> 06/04/18,
> > 5:15:08 PM
> >
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Re: [gmx-users] md simulation of oil hydrocarbon

[Vytautas Rakeviius]

 I think you should check as others did ex.: Optimization of the OPLS-AA Force 
Field for Long Hydrocarbons J. Chem. Theory Comput., 2012, 8 (4), pp 1459–1470
 
On Monday, May 28, 2018, 8:23:50 PM GMT+3, Atila Petrosian 
 wrote:  
 
 Hi all,

I want to do md simulation of oil hydrocarbon?

Is there appropriate force field for these hydrocarbons in gromacs?

What I see in gromacs force fields only was related to aminoacids and
nucleotides.

What is your suggestion for md simulation of oil hydrocarbon?

Best,
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Re: [gmx-users] Doubts in visualisation of sdf output

[Justin Lemkul]

On 6/4/18 7:05 AM, Apramita Chand wrote:

Dear All,
I want the SDF of urea as well as water molecules around my peptide
molecule. For this purpose , I used trjconv to get traj1.xtc with -fit
rot+trans option(selecting peptide as fitting option and system as output).
Using this traj1.xtc, I generated traj2.xtc with centering the peptide and
again system as output.
On this traj2.xtc, I used g_spatial where I selected Peptide molecule for
SDF and then water molecules to output coordinates.


You want the opposite of that - solvent for SDF and peptide for 
coordinate output.


-Justin


The grid.cube files for water and also urea have been formed.
However, how do I visualise the peptide molecule along with the isosurface?
Should I load a separate file containing only centered peptide coordinates?
Should that be .gro file for the entire trajectory?

Please advise.

Yours sincerely,
Apramita


--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] spc.itp file and flexspc.itp

[Justin Lemkul]

On 6/4/18 6:13 AM, Anjana Jayasinghe wrote:

Dear Gromacs Users,
Is there any difference in the simulation, if we define the spc.itp as,

| #ifdef FLEX_SPC |
|  | #include "flexspc.itp" |
|  | #else |
|  | #include "spc.itp" |
|  | #endif |


instead of using the single line  #include "spc.itp" ?
Can anyone help me to understand the difference?


Have you looked at the contents of flexspc.itp? You'll note that it has 
no functional content as this was an old way of defining flexible water. 
Don't do what you have shown above. If you want flexible water, use 
"define = -DFLEXIBLE" and the normal spc.itp in your topology. Again, 
inspect that file's contents to understand what it is doing.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] related to box dimension : solvate protein-ligand complex

[Justin Lemkul]

On 6/4/18 4:19 AM, Quyen V. Vu wrote:

Hi,
As i know that vmd cannot understand dodecahedron, he will take 3 numbers
and plot a cubic while your box still is dodecahedron



VMD will display whatever coordinates it is given. GROMACS will, by 
default, write coordinates using a triclinic representation of the unit 
cell. One can "unwrap" the coordinates with trjconv, and in that case, 
VMD will display exactly the unit cell shape that is defined, and it 
certainly understands dodecahedral and octahedral shapes.


-Justin


On Fri, Jun 1, 2018, 06:48 Seketoulie Keretsu  wrote:


Dear All,

I am doing he Protein-ligand complex tutorial on gromacs 5.0.7 (newly
installed). I have successfully completed this tutorial earlier on
gromacs 4.6.

After the solvation step I found out that the protein-ligand complex
solvated system had a cubic shape while my box dimension (shown using
vmd command: pbc box) adopted a dodecahedron like shape. Please check
the attachment for details.

What could be the possible reason behind this? Kindly advise to
rectify the problem.

The was no error or warning uptill this.

Thank you.

Sincerely,

Seke
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Re: [gmx-users] gangle command

[Justin Lemkul]

On 6/3/18 8:50 AM, delara aghaie wrote:

  Dear Gromacs users
I want to calculate the angle between P-N vector in the head group of DPPC 
molecules with the z-axis (bilayer normal) using gangle command.I know that for 
the z axis I should use (-g2 z) but do not know how to define a vector for P-N. 
Your help would be greatly appreciated.


What have you tried? What did you get? Can you get a sensible result 
with defining an index group with the P and N atoms of a single lipid? 
What about multiple?


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] Distance between the atoms greater than Box length

[Dilip.H.N]

Hello all,
I have extracted the trajectory of my system containing all the water
molecules and my box length is 2.48 ~2.5 nm.
The command was:
gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrjwater500.gro -dt
60  #i have 6 frames (30ns is the time and saved the coordinates
for 0.5 ps )and i have extracted a total of 500 frames trajectory (-dt 60
=>3/500).

And i have written a code which calculates the inter-atomic distance (in my
case it is inter oxygen distances). And when i calculate it (using the
distance formula ie.,
{sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
atom of say, 7SOL and 6SOL, the distance comes to 3.4520.

Here are the coordinates for two water coordinates as representative...

Generated by trjconv : Glycine-Water t=   0.0
xxx
.
.
.
6SOL OW   13   2.405   0.185   1.774
6SOLHW1   14   2.452   0.097   1.782
6SOLHW2   15   2.466   0.259   1.804
7SOL OW   16   0.016   2.177   0.277
7SOLHW1   17   0.098   2.141   0.234
7SOLHW2   18  -0.064   2.126   0.245
.
.
2.49238   2.49238   2.49238

How is this possible ie., 3.452 nm, which is greater than the box length
(2.5 nm). How can the interatomic distance be greater than the box
length..??

Any suggestions are appreciated.

Thank you.

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notified by
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06/04/18,
5:26:50 PM

---
With Best Regards,

Dilip.H.N
PhD Student.

On Mon, Jun 4, 2018 at 5:15 PM, Dilip.H.N  wrote:

> Hello all,
> I have extracted the trajectory of my system containing all the water
> molecules and my box length is 2.48 ~2.5 nm.
>
> And i have written a code which calculates the inter-atomic distance (in
> my case it is inter oxygen distances). And when i calculate it (using the
> distance formula ie.,
> {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
> of say
> 6SOL OW   13   2.405   0.185   1.774
> 6SOLHW1   14   2.452   0.097   1.782
> 6SOLHW2   15   2.466   0.259   1.804
> 7SOL OW   16   0.016   2.177   0.277
> 7SOLHW1   17   0.098   2.141   0.234
> 7SOLHW2   18  -0.064   2.126   0.245
>
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
> [image: Mailtrack]
> 
>  Sender
> notified by
> Mailtrack
> 
>  06/04/18,
> 5:15:08 PM
>
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Re: [gmx-users] define = -DPOSRES_B??

[Justin Lemkul]

On 6/3/18 7:55 AM, m g wrote:

Dear Justin,I fellow your tutorial " Umbrella Sampling", I want to pull a protein across 
the membrane but I don't know how set the "define" section.


What you need to do does not require any special restraints. See 
previous posts on this topic. The restraints used in the tutorial are 
unique to that type of system; please read the article linked from the 
tutorial and references therein to understand why we did what we did.


-Justin


This is my pull code:pull                    = yespull_ngroups            = 
2pull_ncoords            = 1pull_group1_name        = DPPCpull_group2_name        
= Proteinpull_coord1_type        = umbrella      ; harmonic biasing 
forcepull_coord1_geometry    = direction      ; simple distance 
increasepull_coord1_groups      = 1 2pull-coord1-vec         = 0 0 
1pull_coord1_rate        = 0.005          ; 0.005 nm per ps = 5 nm per 
nspull_coord1_k           = 700          ; kJ mol^-1 nm^-2pull_coord1_start       
= yes           ; define initial COM distance > 0
would you please help me?best regards, Ganj


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] Distance between the atoms greater than Box length

[Dilip.H.N]

Hello all,
I have extracted the trajectory of my system containing all the water
molecules and my box length is 2.48 ~2.5 nm.

And i have written a code which calculates the inter-atomic distance (in my
case it is inter oxygen distances). And when i calculate it (using the
distance formula ie.,
{sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
of say
6SOL OW   13   2.405   0.185   1.774
6SOLHW1   14   2.452   0.097   1.782
6SOLHW2   15   2.466   0.259   1.804
7SOL OW   16   0.016   2.177   0.277
7SOLHW1   17   0.098   2.141   0.234
7SOLHW2   18  -0.064   2.126   0.245


---
With Best Regards,

Dilip.H.N
PhD Student.
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5:15:08 PM
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Re: [gmx-users] Groove width

[spss4]

 - Message from rajendra kumar  -
    Date: Mon, 4 Jun 2018 12:23:56 +0200
    From: rajendra kumar 
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Groove width
      To: Discussion list for GROMACS users 


I am doing simulation of DNA molecule. I want to calculate groove width
of
DNA in GROMACS. How to do this? Someone please help.
 


​You may use do_x3dna (http://do-x3dna.readthedocs.io). It uses 3DNA in
background and works with GROMACS files.​ Package also includes tools

to

analyze the large data generated from MD trajectories.
--
Hii
I have tried installation of do_x3dna in ubuntu system following the
instructions given in the link. Installation done successfully then I
have written the path of do_x3dna in .bashrc file(export
do_x3dna=/usr/local/do_x3dna/bin/) and source the file source ~/.bashrc.
Then I tried doing do_x3dna -h but it shows do_x3dna not found. What is
wrong here? My GROMACS version is 2016.3 . Need suggestion .

sunipa



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Re: [gmx-users] Groove width

[spss4]

Hii
I have tried installation of do_x3dna in ubuntu system following the
instructions given in the link. Installation done successfully then I
have written the path of do_x3dna in .bashrc file(export
do_x3dna=/usr/local/do_x3dna/bin/) and source the file source ~/.bashrc.
Then I tried doing do_x3dna -h but it shows do_x3dna not found. What is
wrong here? My GROMACS version is 2016.3 . Need suggestion .

Sunipa

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[gmx-users] Fwd: Centering a molecule

[spss4]

Hi all
I want to center my molecule into a rectangular box after final mdrun by
GROMACS. I am using the following command:
gmx trjconv -f  traj.trr -s md.tpr -center -pbc  mol -b 100 -e 120 -o 
test.gro 
But output  shown is still out of the box. This command works for cubic
box. Is there anything different flag for rectangular box? My box size is
5 5 7.

Thanks
Sunipa
--- Begin Message ---

Hi all
I want to center my molecule into a rectangular box by GROMACS. I am using
the following command:
gmx trjconv -f  traj.trr -s md.tpr -center -pbc  mol -b 100 -e 120 -o 
test.gro 
But output  shown is still out of the box. This command works for cubic
box. Is there anything different flag for rectangular box? My box size is
5 5 7.

Thanks
Sunipa
--- End Message ---
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[gmx-users] Doubts in visualisation of sdf output

[Apramita Chand]

Dear All,
I want the SDF of urea as well as water molecules around my peptide
molecule. For this purpose , I used trjconv to get traj1.xtc with -fit
rot+trans option(selecting peptide as fitting option and system as output).
Using this traj1.xtc, I generated traj2.xtc with centering the peptide and
again system as output.
On this traj2.xtc, I used g_spatial where I selected Peptide molecule for
SDF and then water molecules to output coordinates.
The grid.cube files for water and also urea have been formed.
However, how do I visualise the peptide molecule along with the isosurface?
Should I load a separate file containing only centered peptide coordinates?
Should that be .gro file for the entire trajectory?

Please advise.

Yours sincerely,
Apramita
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Re: [gmx-users] Groove width

[rajendra kumar]

>
>
> I am doing simulation of DNA molecule. I want to calculate groove width of
> DNA in GROMACS. How to do this? Someone please help.
>
>
​You may use do_x3dna (http://do-x3dna.readthedocs.io). It uses 3DNA in
background and works with GROMACS files.​ Package also includes tools to
analyze the large data generated from MD trajectories.
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[gmx-users] spc.itp file and flexspc.itp

[Anjana Jayasinghe]

Dear Gromacs Users,
Is there any difference in the simulation, if we define the spc.itp as,

| #ifdef FLEX_SPC |
|  | #include "flexspc.itp" |
|  | #else |
|  | #include "spc.itp" |
|  | #endif |


instead of using the single line  #include "spc.itp" ?
Can anyone help me to understand the difference?
Thank you.





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Re: [gmx-users] Box dimension

[rose rahmani]

It's ZnS and yes it's periodic and in water not in vaccum. I used DFT just
for optimization and obtaining charges.  I did this job for an slab before.
I mean the AA was between slab surface and wall but it was the vaccum space
before slab and after wall. imagine this structures in a box of z=12. The
slab was in z=4 and wall in z=7.5 and WATER between z=4 to7.5  So z=0
to 4 and 7.5 to 12 is in vaccum. and AA is between z=4 to 7.5 .
I think it's clear now.

Best regards
-Rose

On Mon, 4 Jun 2018, 13:37 Alex,  wrote:

> It's a bit unclear what's happening in your system. Are you simulating
> in vacuum, or in solvent? I am assuming it's in solvent and that the
> word "vacuum" simply means space unoccupied by the structure, i.e. a
> term used by DFT folks. With all nanotubes (carbon, ZnS, BN, etc), water
> forms various interfaces at the boundary, so simply look at the
> interface data and/or other literature and see roughly how much space is
> needed to accommodate that in addition to everything else.
>
> Yes, people do put their NTs between walls with a periodic boundary,
> which requires that the nanotube edges are crystallographically
> periodic, i.e. fits a supercell. It is a very useful practice.
>
> Alex
>
>
> On 6/4/2018 2:48 AM, rose rahmani wrote:
> > Sorry i should correct myself
> >
> > On Mon, 4 Jun 2018, 13:10 rose rahmani,  wrote:
> >
> >> I have nothing to say...
> >> but i'm a beginner and i comment here to have your ideas as experienced.
> >>   It's not CNT. It's an inorganic nanotube which its partial atomic
> charges
> >> (0.48 , -0.48) is calculated by DFT.
> >>
> >> When i optimized structure in other packages i put it in box with Z=3.
> So
> >> first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
> >> z=2.15 and the "COM" is in z=1.5 .
> >> So NT outer curvature which is in touch with AA is in z=2.15(0.85 + 1.3)
> >> Did you calculate these arithmetics when the z dimension of CNT started
> >> from z=0 to z=1.3?
> >>
> >> People sometimes put NT between 2 walls? As the z=7 need much more water
> >> and long calculations. Do you think put NT between two walls and use
> vaccum
> >>
> > Use box 3times distances between two walls so the vaccum is 2/3 this
> > distance
> >
> >> 3times distances between walls is better
> >>
> > than multiply 2 to keep it symmetric?(now you have 1.3 + 2*1.5 +
> thickness
> >> of two walls) how do you think, sir?
> >>
> >> With regards
> >> -Rose
> >>
> >>
> >>
> >>
> >> On 4 Jun 2018 12:04, "Alex"  wrote:
> >>
> >> I'm kind and civil, practically a sweetheart. I just can't put smiley
> >> faces everywhere! On the other hand, it does not hurt to try things and
> >> have a little bit of initiative. I don't know why I am telling you this,
> >> like you've never supervised students... Also, CNTs are simulated
> >> exactly the same way (within these forcefield flavors) as pretty much
> >> anything else you can think of. That is, until one day when you guys
> >> decide to come with a testing Gromacs version that includes FFs not
> >> relying on permanent topologies. ;)
> >>
> >>
> >> Alex
> >>
> >>
> >>
> >> On 6/4/2018 1:28 AM, Mark Abraham wrote:
> >>> Hi,
> >>>
> >>> Let's keep the discussion kind and civil, please. What's obvious when
> you
> >>> have experience often isn't when you are new. :-) I sure don't
> understand
> >>> the arithmetic involved, but then I've never attempted a CNT
> simulation!
> >>>
> >>> Mark
> >>>
> >>> On Mon, Jun 4, 2018, 09:08 Alex  wrote:
> >>>
>  And again, your question has nothing to do with Gromacs. It has to do
>  with what you want to do, common sense, and basic arithmetic.
> 
>  CNTs interact at pretty short range (if they are intact and without
> edge
>  passivation), so I'd just go with a distance sweep range of ~1.5 nm
> and
>  give it some additional space, say, 1 nm, and finally keep the box
>  symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1)
> x
>  2 = 7.6 nm. You could of course place the CNT off center (in Z) to
>  shorten the box.
> 
>  Alex
> 
> 
>  On 6/4/2018 12:53 AM, rose rahmani wrote:
> > Hi,
> >
> > I want to do umbrella sampling for different coordination of amino
> acid
> > through different distances (in Z dimension) from nanotube. The
> >> nanotube
> > axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
> > curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
> > (because the nanotube radius is 0.65nm). The initial distance of
> amino
>  acid
> > from nanotube is 2nm. The question is how should i choose the box Z
> > dimension that some artifacts (justin explained in tutorial) doesn't
> > happen? I choose 7nm, is it ok or large?
> >
> > Would you please help me?
> >
> > Best regards
> > -Rose
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Re: [gmx-users] Box dimension

[Alex]

It's a bit unclear what's happening in your system. Are you simulating 
in vacuum, or in solvent? I am assuming it's in solvent and that the 
word "vacuum" simply means space unoccupied by the structure, i.e. a 
term used by DFT folks. With all nanotubes (carbon, ZnS, BN, etc), water 
forms various interfaces at the boundary, so simply look at the 
interface data and/or other literature and see roughly how much space is 
needed to accommodate that in addition to everything else.


Yes, people do put their NTs between walls with a periodic boundary, 
which requires that the nanotube edges are crystallographically 
periodic, i.e. fits a supercell. It is a very useful practice.


Alex


On 6/4/2018 2:48 AM, rose rahmani wrote:

Sorry i should correct myself

On Mon, 4 Jun 2018, 13:10 rose rahmani,  wrote:


I have nothing to say...
but i'm a beginner and i comment here to have your ideas as experienced.
  It's not CNT. It's an inorganic nanotube which its partial atomic charges
(0.48 , -0.48) is calculated by DFT.

When i optimized structure in other packages i put it in box with Z=3. So
first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
z=2.15 and the "COM" is in z=1.5 .
So NT outer curvature which is in touch with AA is in z=2.15(0.85 + 1.3)
Did you calculate these arithmetics when the z dimension of CNT started
from z=0 to z=1.3?

People sometimes put NT between 2 walls? As the z=7 need much more water
and long calculations. Do you think put NT between two walls and use vaccum


Use box 3times distances between two walls so the vaccum is 2/3 this
distance


3times distances between walls is better


than multiply 2 to keep it symmetric?(now you have 1.3 + 2*1.5 + thickness

of two walls) how do you think, sir?

With regards
-Rose




On 4 Jun 2018 12:04, "Alex"  wrote:

I'm kind and civil, practically a sweetheart. I just can't put smiley
faces everywhere! On the other hand, it does not hurt to try things and
have a little bit of initiative. I don't know why I am telling you this,
like you've never supervised students... Also, CNTs are simulated
exactly the same way (within these forcefield flavors) as pretty much
anything else you can think of. That is, until one day when you guys
decide to come with a testing Gromacs version that includes FFs not
relying on permanent topologies. ;)


Alex



On 6/4/2018 1:28 AM, Mark Abraham wrote:

Hi,

Let's keep the discussion kind and civil, please. What's obvious when you
have experience often isn't when you are new. :-) I sure don't understand
the arithmetic involved, but then I've never attempted a CNT simulation!

Mark

On Mon, Jun 4, 2018, 09:08 Alex  wrote:


And again, your question has nothing to do with Gromacs. It has to do
with what you want to do, common sense, and basic arithmetic.

CNTs interact at pretty short range (if they are intact and without edge
passivation), so I'd just go with a distance sweep range of ~1.5 nm and
give it some additional space, say, 1 nm, and finally keep the box
symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
2 = 7.6 nm. You could of course place the CNT off center (in Z) to
shorten the box.

Alex


On 6/4/2018 12:53 AM, rose rahmani wrote:

Hi,

I want to do umbrella sampling for different coordination of amino acid
through different distances (in Z dimension) from nanotube. The

nanotube

axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
(because the nanotube radius is 0.65nm). The initial distance of amino

acid

from nanotube is 2nm. The question is how should i choose the box Z
dimension that some artifacts (justin explained in tutorial) doesn't
happen? I choose 7nm, is it ok or large?

Would you please help me?

Best regards
-Rose

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Re: [gmx-users] Box dimension

[rose rahmani]

Sorry i should correct myself

On Mon, 4 Jun 2018, 13:10 rose rahmani,  wrote:

> I have nothing to say...
> but i'm a beginner and i comment here to have your ideas as experienced.
>  It's not CNT. It's an inorganic nanotube which its partial atomic charges
> (0.48 , -0.48) is calculated by DFT.
>
> When i optimized structure in other packages i put it in box with Z=3. So
> first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
> z=2.15 and the "COM" is in z=1.5 .
> So NT outer curvature which is in touch with AA is in z=2.15(0.85 + 1.3)
> Did you calculate these arithmetics when the z dimension of CNT started
> from z=0 to z=1.3?
>
> People sometimes put NT between 2 walls? As the z=7 need much more water
> and long calculations. Do you think put NT between two walls and use vaccum
>
Use box 3times distances between two walls so the vaccum is 2/3 this
distance

> 3times distances between walls is better
>
than multiply 2 to keep it symmetric?(now you have 1.3 + 2*1.5 + thickness
> of two walls) how do you think, sir?
>
> With regards
> -Rose
>
>
>
>
> On 4 Jun 2018 12:04, "Alex"  wrote:
>
> I'm kind and civil, practically a sweetheart. I just can't put smiley
> faces everywhere! On the other hand, it does not hurt to try things and
> have a little bit of initiative. I don't know why I am telling you this,
> like you've never supervised students... Also, CNTs are simulated
> exactly the same way (within these forcefield flavors) as pretty much
> anything else you can think of. That is, until one day when you guys
> decide to come with a testing Gromacs version that includes FFs not
> relying on permanent topologies. ;)
>
>
> Alex
>
>
>
> On 6/4/2018 1:28 AM, Mark Abraham wrote:
> > Hi,
> >
> > Let's keep the discussion kind and civil, please. What's obvious when you
> > have experience often isn't when you are new. :-) I sure don't understand
> > the arithmetic involved, but then I've never attempted a CNT simulation!
> >
> > Mark
> >
> > On Mon, Jun 4, 2018, 09:08 Alex  wrote:
> >
> >> And again, your question has nothing to do with Gromacs. It has to do
> >> with what you want to do, common sense, and basic arithmetic.
> >>
> >> CNTs interact at pretty short range (if they are intact and without edge
> >> passivation), so I'd just go with a distance sweep range of ~1.5 nm and
> >> give it some additional space, say, 1 nm, and finally keep the box
> >> symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
> >> 2 = 7.6 nm. You could of course place the CNT off center (in Z) to
> >> shorten the box.
> >>
> >> Alex
> >>
> >>
> >> On 6/4/2018 12:53 AM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> I want to do umbrella sampling for different coordination of amino acid
> >>> through different distances (in Z dimension) from nanotube. The
> nanotube
> >>> axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
> >>> curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
> >>> (because the nanotube radius is 0.65nm). The initial distance of amino
> >> acid
> >>> from nanotube is 2nm. The question is how should i choose the box Z
> >>> dimension that some artifacts (justin explained in tutorial) doesn't
> >>> happen? I choose 7nm, is it ok or large?
> >>>
> >>> Would you please help me?
> >>>
> >>> Best regards
> >>> -Rose
> >> --
> >> 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
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
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Re: [gmx-users] Box dimension

[rose rahmani]

I have nothing to say...
but i'm a beginner and i comment here to have your ideas as experienced.
 It's not CNT. It's an inorganic nanotube which its partial atomic charges
(0.48 , -0.48) is calculated by DFT.

When i optimized structure in other packages i put it in box with Z=3. So
first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
z=2.15 and the "COM" is in z=1.5 .
So NT outer curvature which is in touch with AA is in z=2.15(0.85 + 1.3)
Did you calculate these arithmetics when the z dimension of CNT started
from z=0 to z=1.3?

People sometimes put NT between 2 walls? As the z=7 need much more water
and long calculations. Do you think put NT between two walls and use vaccum
3times distances between walls is better than multiply 2 to keep it
symmetric?(now you have 1.3 + 2*1.5 + thickness of two walls) how do you
think, sir?

With regards
-Rose




On 4 Jun 2018 12:04, "Alex"  wrote:

I'm kind and civil, practically a sweetheart. I just can't put smiley
faces everywhere! On the other hand, it does not hurt to try things and
have a little bit of initiative. I don't know why I am telling you this,
like you've never supervised students... Also, CNTs are simulated
exactly the same way (within these forcefield flavors) as pretty much
anything else you can think of. That is, until one day when you guys
decide to come with a testing Gromacs version that includes FFs not
relying on permanent topologies. ;)


Alex



On 6/4/2018 1:28 AM, Mark Abraham wrote:
> Hi,
>
> Let's keep the discussion kind and civil, please. What's obvious when you
> have experience often isn't when you are new. :-) I sure don't understand
> the arithmetic involved, but then I've never attempted a CNT simulation!
>
> Mark
>
> On Mon, Jun 4, 2018, 09:08 Alex  wrote:
>
>> And again, your question has nothing to do with Gromacs. It has to do
>> with what you want to do, common sense, and basic arithmetic.
>>
>> CNTs interact at pretty short range (if they are intact and without edge
>> passivation), so I'd just go with a distance sweep range of ~1.5 nm and
>> give it some additional space, say, 1 nm, and finally keep the box
>> symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
>> 2 = 7.6 nm. You could of course place the CNT off center (in Z) to
>> shorten the box.
>>
>> Alex
>>
>>
>> On 6/4/2018 12:53 AM, rose rahmani wrote:
>>> Hi,
>>>
>>> I want to do umbrella sampling for different coordination of amino acid
>>> through different distances (in Z dimension) from nanotube. The nanotube
>>> axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
>>> curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
>>> (because the nanotube radius is 0.65nm). The initial distance of amino
>> acid
>>> from nanotube is 2nm. The question is how should i choose the box Z
>>> dimension that some artifacts (justin explained in tutorial) doesn't
>>> happen? I choose 7nm, is it ok or large?
>>>
>>> Would you please help me?
>>>
>>> Best regards
>>> -Rose
>> --
>> 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.
>>

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[gmx-users] Centering the molecule

[spss4]

Hi all
I want to center my molecule into a rectangular box by GROMACS. I am using
the following command:
gmx trjconv -f  traj.trr -s md.tpr -center -pbc  mol -b 100 -e 120 -o 
test.gro 
But output  shown is still out of the box. This command works for cubic
box. Is there anything different flag for rectangular box? My box size is
5 5 7.

Thanks
Sunipa
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Re: [gmx-users] Groove width

[spss4]

 Hii David
    I want to see if there is any change in the groove width in presence
of different solvents. I thing this can give me some information of DNA
structural change if it is happening in that particular solvent.
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Re: [gmx-users] related to box dimension : solvate protein-ligand complex

[Quyen V. Vu]

Hi,
As i know that vmd cannot understand dodecahedron, he will take 3 numbers
and plot a cubic while your box still is dodecahedron


On Fri, Jun 1, 2018, 06:48 Seketoulie Keretsu  wrote:

> Dear All,
>
> I am doing he Protein-ligand complex tutorial on gromacs 5.0.7 (newly
> installed). I have successfully completed this tutorial earlier on
> gromacs 4.6.
>
> After the solvation step I found out that the protein-ligand complex
> solvated system had a cubic shape while my box dimension (shown using
> vmd command: pbc box) adopted a dodecahedron like shape. Please check
> the attachment for details.
>
> What could be the possible reason behind this? Kindly advise to
> rectify the problem.
>
> The was no error or warning uptill this.
>
> Thank you.
>
> Sincerely,
>
> Seke
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Re: [gmx-users] Groove width

[spss4]

 


Thank you for your suggestion. This is a new thing I am learning.
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Re: [gmx-users] Box dimension

[Alex]

I will be using more smileys, I promise -- especially given how often I 
post. You know how wrong Landau was when he said: "Doing science out of 
politeness always results in complete lack of science AND politeness." A 
rude person that guy was!


By the way, those postdocs, they should check out the LAMMPS board and 
see what Axel Kohlmeyer does when you ask a question. ;)


Alex


On 6/4/2018 1:47 AM, Mark Abraham wrote:

Hi,

Let's be clear - so called common sense is the product of experience, and
new people should not be expected to have it. They can be expected to have
tried to solve their own problem :-) The first part of your answer looks
like it addressed your frustration, not the question. Your actual answer
included a tidbit about knowing that they act at a specific short range...

We hear that even post docs are sometimes too afraid too post here, which
is a sorry loss for everyone. I would like us all to think how to improve
ourselves a little :-)

Mark

On Mon, Jun 4, 2018, 09:34 Alex  wrote:


I'm kind and civil, practically a sweetheart. I just can't put smiley
faces everywhere! On the other hand, it does not hurt to try things and
have a little bit of initiative. I don't know why I am telling you this,
like you've never supervised students... Also, CNTs are simulated
exactly the same way (within these forcefield flavors) as pretty much
anything else you can think of. That is, until one day when you guys
decide to come with a testing Gromacs version that includes FFs not
relying on permanent topologies. ;)

Alex


On 6/4/2018 1:28 AM, Mark Abraham wrote:

Hi,

Let's keep the discussion kind and civil, please. What's obvious when you
have experience often isn't when you are new. :-) I sure don't understand
the arithmetic involved, but then I've never attempted a CNT simulation!

Mark

On Mon, Jun 4, 2018, 09:08 Alex  wrote:


And again, your question has nothing to do with Gromacs. It has to do
with what you want to do, common sense, and basic arithmetic.

CNTs interact at pretty short range (if they are intact and without edge
passivation), so I'd just go with a distance sweep range of ~1.5 nm and
give it some additional space, say, 1 nm, and finally keep the box
symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
2 = 7.6 nm. You could of course place the CNT off center (in Z) to
shorten the box.

Alex


On 6/4/2018 12:53 AM, rose rahmani wrote:

Hi,

I want to do umbrella sampling for different coordination of amino acid
through different distances (in Z dimension) from nanotube. The

nanotube

axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
(because the nanotube radius is 0.65nm). The initial distance of amino

acid

from nanotube is 2nm. The question is how should i choose the box Z
dimension that some artifacts (justin explained in tutorial) doesn't
happen? I choose 7nm, is it ok or large?

Would you please help me?

Best regards
-Rose

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Re: [gmx-users] Box dimension

[Mark Abraham]

Hi,

Let's be clear - so called common sense is the product of experience, and
new people should not be expected to have it. They can be expected to have
tried to solve their own problem :-) The first part of your answer looks
like it addressed your frustration, not the question. Your actual answer
included a tidbit about knowing that they act at a specific short range...

We hear that even post docs are sometimes too afraid too post here, which
is a sorry loss for everyone. I would like us all to think how to improve
ourselves a little :-)

Mark

On Mon, Jun 4, 2018, 09:34 Alex  wrote:

> I'm kind and civil, practically a sweetheart. I just can't put smiley
> faces everywhere! On the other hand, it does not hurt to try things and
> have a little bit of initiative. I don't know why I am telling you this,
> like you've never supervised students... Also, CNTs are simulated
> exactly the same way (within these forcefield flavors) as pretty much
> anything else you can think of. That is, until one day when you guys
> decide to come with a testing Gromacs version that includes FFs not
> relying on permanent topologies. ;)
>
> Alex
>
>
> On 6/4/2018 1:28 AM, Mark Abraham wrote:
> > Hi,
> >
> > Let's keep the discussion kind and civil, please. What's obvious when you
> > have experience often isn't when you are new. :-) I sure don't understand
> > the arithmetic involved, but then I've never attempted a CNT simulation!
> >
> > Mark
> >
> > On Mon, Jun 4, 2018, 09:08 Alex  wrote:
> >
> >> And again, your question has nothing to do with Gromacs. It has to do
> >> with what you want to do, common sense, and basic arithmetic.
> >>
> >> CNTs interact at pretty short range (if they are intact and without edge
> >> passivation), so I'd just go with a distance sweep range of ~1.5 nm and
> >> give it some additional space, say, 1 nm, and finally keep the box
> >> symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
> >> 2 = 7.6 nm. You could of course place the CNT off center (in Z) to
> >> shorten the box.
> >>
> >> Alex
> >>
> >>
> >> On 6/4/2018 12:53 AM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> I want to do umbrella sampling for different coordination of amino acid
> >>> through different distances (in Z dimension) from nanotube. The
> nanotube
> >>> axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
> >>> curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
> >>> (because the nanotube radius is 0.65nm). The initial distance of amino
> >> acid
> >>> from nanotube is 2nm. The question is how should i choose the box Z
> >>> dimension that some artifacts (justin explained in tutorial) doesn't
> >>> happen? I choose 7nm, is it ok or large?
> >>>
> >>> Would you please help me?
> >>>
> >>> Best regards
> >>> -Rose
> >> --
> >> 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.
> >>
>
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Re: [gmx-users] Box dimension

[Alex]

I'm kind and civil, practically a sweetheart. I just can't put smiley 
faces everywhere! On the other hand, it does not hurt to try things and 
have a little bit of initiative. I don't know why I am telling you this, 
like you've never supervised students... Also, CNTs are simulated 
exactly the same way (within these forcefield flavors) as pretty much 
anything else you can think of. That is, until one day when you guys 
decide to come with a testing Gromacs version that includes FFs not 
relying on permanent topologies. ;)


Alex


On 6/4/2018 1:28 AM, Mark Abraham wrote:

Hi,

Let's keep the discussion kind and civil, please. What's obvious when you
have experience often isn't when you are new. :-) I sure don't understand
the arithmetic involved, but then I've never attempted a CNT simulation!

Mark

On Mon, Jun 4, 2018, 09:08 Alex  wrote:


And again, your question has nothing to do with Gromacs. It has to do
with what you want to do, common sense, and basic arithmetic.

CNTs interact at pretty short range (if they are intact and without edge
passivation), so I'd just go with a distance sweep range of ~1.5 nm and
give it some additional space, say, 1 nm, and finally keep the box
symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
2 = 7.6 nm. You could of course place the CNT off center (in Z) to
shorten the box.

Alex


On 6/4/2018 12:53 AM, rose rahmani wrote:

Hi,

I want to do umbrella sampling for different coordination of amino acid
through different distances (in Z dimension) from nanotube. The nanotube
axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
(because the nanotube radius is 0.65nm). The initial distance of amino

acid

from nanotube is 2nm. The question is how should i choose the box Z
dimension that some artifacts (justin explained in tutorial) doesn't
happen? I choose 7nm, is it ok or large?

Would you please help me?

Best regards
-Rose

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Re: [gmx-users] Box dimension

[Mark Abraham]

Hi,

Let's keep the discussion kind and civil, please. What's obvious when you
have experience often isn't when you are new. :-) I sure don't understand
the arithmetic involved, but then I've never attempted a CNT simulation!

Mark

On Mon, Jun 4, 2018, 09:08 Alex  wrote:

> And again, your question has nothing to do with Gromacs. It has to do
> with what you want to do, common sense, and basic arithmetic.
>
> CNTs interact at pretty short range (if they are intact and without edge
> passivation), so I'd just go with a distance sweep range of ~1.5 nm and
> give it some additional space, say, 1 nm, and finally keep the box
> symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
> 2 = 7.6 nm. You could of course place the CNT off center (in Z) to
> shorten the box.
>
> Alex
>
>
> On 6/4/2018 12:53 AM, rose rahmani wrote:
> > Hi,
> >
> > I want to do umbrella sampling for different coordination of amino acid
> > through different distances (in Z dimension) from nanotube. The nanotube
> > axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
> > curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
> > (because the nanotube radius is 0.65nm). The initial distance of amino
> acid
> > from nanotube is 2nm. The question is how should i choose the box Z
> > dimension that some artifacts (justin explained in tutorial) doesn't
> > happen? I choose 7nm, is it ok or large?
> >
> > Would you please help me?
> >
> > Best regards
> > -Rose
>
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Re: [gmx-users] Box dimension

[Alex]

And again, your question has nothing to do with Gromacs. It has to do 
with what you want to do, common sense, and basic arithmetic.


CNTs interact at pretty short range (if they are intact and without edge 
passivation), so I'd just go with a distance sweep range of ~1.5 nm and 
give it some additional space, say, 1 nm, and finally keep the box 
symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x 
2 = 7.6 nm. You could of course place the CNT off center (in Z) to 
shorten the box.


Alex


On 6/4/2018 12:53 AM, rose rahmani wrote:

Hi,

I want to do umbrella sampling for different coordination of amino acid
through different distances (in Z dimension) from nanotube. The nanotube
axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
(because the nanotube radius is 0.65nm). The initial distance of amino acid
from nanotube is 2nm. The question is how should i choose the box Z
dimension that some artifacts (justin explained in tutorial) doesn't
happen? I choose 7nm, is it ok or large?

Would you please help me?

Best regards
-Rose


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