Re: [gmx-users] Gromacs 2018 and GPU

[Justin Lemkul]

On 5/4/18 6:53 PM, paul buscemi wrote:

Justin,

Here is the install script  and a snippit from the log file .

Gromacs runs normally with this ( fresh ) install but without GPU use

Paul

cmake .. -DGMX_BUILD_OWN_FFTW=ON \
  -DGMX_GPU=on   \
  -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit \
 -DGMX_USE_OPENCL=on

Command line:
   gmx mdrun -deffnm md_0_1

GROMACS version:VERSION 5.1.2
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:disabled


Well, here's what you need to know. Something failed in trying to enable 
GPU acceleration. Take a look at the cmake output.


-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] Gromacs 2018 and GPU

[paul buscemi]

Justin,

Here is the install script  and a snippit from the log file .  

Gromacs runs normally with this ( fresh ) install but without GPU use

Paul

cmake .. -DGMX_BUILD_OWN_FFTW=ON \
 -DGMX_GPU=on   \
 -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit \
-DGMX_USE_OPENCL=on  

Command line:
  gmx mdrun -deffnm md_0_1

GROMACS version:VERSION 5.1.2
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:disabled
OpenCL support: disabled
invsqrt routine:gmx_software_invsqrt(x)
SIMD instructions:  SSE2
FFT library:fftw-3.3.4-sse2-avx
RDTSCP usage:   enabled
C++11 compilation:  enabled
TNG support:enabled
Tracing support:disable…..



> On May 4, 2018, at 1:12 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/4/18 2:11 PM, paul buscemi wrote:
>> Thank you Justin.
>> 
>> Not at the linux system at the moment, but is there anything in particular I 
>> should look for in the log file ?
> 
> Just look for "GPU" and you'll find it.
> 
> -Justin
> 
>> Paul
>> 
>>> On 4,May 2018, at 12:55 PM, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 5/4/18 1:48 PM, paul buscemi wrote:
 thank you for the prompt response.  I will check out the link.  Regarding 
 2)  One can immediately determine if the GPU is/is  running since Gromacs 
 tells you at the beginning - in my case - that the CPU’s being used and 
 linux system monitor tells you that all CPU’s are running, - not to 
 mention the fan speed, and nvidia-smi registers no GPU running
 
 What I was asking was for the proper format for invoking the GPU .  I used
 gmx mdrun -deffnm md_0_1 -nb gpu ##   this is from the lysozyme 
 tutorial MD page
 but this starts Gromacs using the CPU’s and was asking if this is a proper 
 format for a single GPU.
>>> With version 2018, you don't even need to use "-nb gpu," mdrun will 
>>> automatically run on the GPU if it is detected properly. As Mark said, 
>>> check your .log file for a full breakdown of how mdrun configured the 
>>> simulation using the available hardware.
>>> 
>>> -Justin
>>> 
 thanks
 Paul
 
> On 4,May 2018, at 11:57 AM, Mark Abraham  wrote:
> 
> Hi,
> 
> On Fri, May 4, 2018 at 6:43 PM paul buscemi  > wrote:
> 
>> I’ve been struggling for a for several days to get Gromacs-2018 to use my
>> GPU.  I followed the INSTALL instructions ( several times ! ) that are
>> provided in the 2018 tarball
>> 
>> I know that the GPU ( GTX1080)  is installed properly in that it works
>> with Schrodinger and the Nvidia self tests.  Gromacs runs the  MD from 
>> the
>> University of Baltimore  lysozyme  example normally
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
>> <
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/>
>> but only on the 8 threads of the  CPU
>> 
> The tutorial explicitly addresses this. See
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html
>  
> 
> 
> 
>> Make test  indicates that it sees the GPU, but
>> 
>> 1)  is there a way to definitively determine if the make commands were 
>> run
>> properly or that Gromacs was installed properly with the GPU
>> 
> To know that a simulation ran on the GPU, you must inspect the log file
> that it wrote.
> 
> 
>> 2) for a linux desktop system with one GPU,  a/the  proper command to run
>> the lysozyme .  I ask since there is indication that with one GPU  (0) it
>> will be dedicated to graphics.
>> 
> If the display is sharing the GPU, then it shares the GPU (and performance
> of either the display or the simulation might be affected). With only one
> GPU, there's no option (unless your motherboard has a built-in GPU that
> you'd prefer to use for the display).
> 
> 
>> 3) is there an up to data set of install instructions for  Gromacs 2018
>> and Nvidia 9.1 toolkit,  384.11 drivers ?
>> 
> No, there's nothing unusual about that, so the generic instructions apply.
> 
> Mark
> 
> 
>> Regards
>> Paul
>> --
>> 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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Re: [gmx-users] gmx with openmpi installed not on root

[Justin Lemkul]

On 5/4/18 2:15 PM, Dariush Mohammadyani wrote:

Hi All,

How can I install gromacs with an openmpi installed in a non-standard path
(not on root)?
Our compute node does not have access to the root.


Tell cmake where to find it with -DCMAKE_C_COMPILER=/path/to/your/mpicc

-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] gmx with openmpi installed not on root

[Dariush Mohammadyani]

Hi All,

How can I install gromacs with an openmpi installed in a non-standard path
(not on root)?
Our compute node does not have access to the root.


Regards,
Dariush
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Re: [gmx-users] Gromacs 2018 and GPU

[Justin Lemkul]

On 5/4/18 2:11 PM, paul buscemi wrote:

Thank you Justin.

Not at the linux system at the moment, but is there anything in particular I 
should look for in the log file ?


Just look for "GPU" and you'll find it.

-Justin


Paul


On 4,May 2018, at 12:55 PM, Justin Lemkul  wrote:



On 5/4/18 1:48 PM, paul buscemi wrote:

thank you for the prompt response.  I will check out the link.  Regarding 2)  
One can immediately determine if the GPU is/is  running since Gromacs tells you 
at the beginning - in my case - that the CPU’s being used and linux system 
monitor tells you that all CPU’s are running, - not to mention the fan speed, 
and nvidia-smi registers no GPU running

What I was asking was for the proper format for invoking the GPU .  I used
gmx mdrun -deffnm md_0_1 -nb gpu ##   this is from the lysozyme tutorial MD 
page
but this starts Gromacs using the CPU’s and was asking if this is a proper 
format for a single GPU.

With version 2018, you don't even need to use "-nb gpu," mdrun will 
automatically run on the GPU if it is detected properly. As Mark said, check your .log 
file for a full breakdown of how mdrun configured the simulation using the available 
hardware.

-Justin


thanks
Paul


On 4,May 2018, at 11:57 AM, Mark Abraham  wrote:

Hi,

On Fri, May 4, 2018 at 6:43 PM paul buscemi > wrote:


I’ve been struggling for a for several days to get Gromacs-2018 to use my
GPU.  I followed the INSTALL instructions ( several times ! ) that are
provided in the 2018 tarball

I know that the GPU ( GTX1080)  is installed properly in that it works
with Schrodinger and the Nvidia self tests.  Gromacs runs the  MD from the
University of Baltimore  lysozyme  example normally
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
<
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/>
but only on the 8 threads of the  CPU


The tutorial explicitly addresses this. See
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html
 




Make test  indicates that it sees the GPU, but

1)  is there a way to definitively determine if the make commands were run
properly or that Gromacs was installed properly with the GPU


To know that a simulation ran on the GPU, you must inspect the log file
that it wrote.



2) for a linux desktop system with one GPU,  a/the  proper command to run
the lysozyme .  I ask since there is indication that with one GPU  (0) it
will be dedicated to graphics.


If the display is sharing the GPU, then it shares the GPU (and performance
of either the display or the simulation might be affected). With only one
GPU, there's no option (unless your motherboard has a built-in GPU that
you'd prefer to use for the display).



3) is there an up to data set of install instructions for  Gromacs 2018
and Nvidia 9.1 toolkit,  384.11 drivers ?


No, there's nothing unusual about that, so the generic instructions apply.

Mark



Regards
Paul
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==

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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
http://www.thelemkullab.com 

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Re: [gmx-users] Gromacs 2018 and GPU

[paul buscemi]

Thank you Justin. 

Not at the linux system at the moment, but is there anything in particular I 
should look for in the log file ?

Paul

> On 4,May 2018, at 12:55 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/4/18 1:48 PM, paul buscemi wrote:
>> thank you for the prompt response.  I will check out the link.  Regarding 2) 
>>  One can immediately determine if the GPU is/is  running since Gromacs tells 
>> you at the beginning - in my case - that the CPU’s being used and linux 
>> system monitor tells you that all CPU’s are running, - not to mention the 
>> fan speed, and nvidia-smi registers no GPU running
>> 
>> What I was asking was for the proper format for invoking the GPU .  I used
>> gmx mdrun -deffnm md_0_1 -nb gpu ##   this is from the lysozyme tutorial 
>> MD page
>> but this starts Gromacs using the CPU’s and was asking if this is a proper 
>> format for a single GPU.
> 
> With version 2018, you don't even need to use "-nb gpu," mdrun will 
> automatically run on the GPU if it is detected properly. As Mark said, check 
> your .log file for a full breakdown of how mdrun configured the simulation 
> using the available hardware.
> 
> -Justin
> 
>> thanks
>> Paul
>> 
>>> On 4,May 2018, at 11:57 AM, Mark Abraham  wrote:
>>> 
>>> Hi,
>>> 
>>> On Fri, May 4, 2018 at 6:43 PM paul buscemi >> > wrote:
>>> 
 
 I’ve been struggling for a for several days to get Gromacs-2018 to use my
 GPU.  I followed the INSTALL instructions ( several times ! ) that are
 provided in the 2018 tarball
 
 I know that the GPU ( GTX1080)  is installed properly in that it works
 with Schrodinger and the Nvidia self tests.  Gromacs runs the  MD from the
 University of Baltimore  lysozyme  example normally
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
 <
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/>
 but only on the 8 threads of the  CPU
 
>>> The tutorial explicitly addresses this. See
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html
>>>  
>>> 
>>> 
>>> 
 Make test  indicates that it sees the GPU, but
 
 1)  is there a way to definitively determine if the make commands were run
 properly or that Gromacs was installed properly with the GPU
 
>>> To know that a simulation ran on the GPU, you must inspect the log file
>>> that it wrote.
>>> 
>>> 
 2) for a linux desktop system with one GPU,  a/the  proper command to run
 the lysozyme .  I ask since there is indication that with one GPU  (0) it
 will be dedicated to graphics.
 
>>> If the display is sharing the GPU, then it shares the GPU (and performance
>>> of either the display or the simulation might be affected). With only one
>>> GPU, there's no option (unless your motherboard has a built-in GPU that
>>> you'd prefer to use for the display).
>>> 
>>> 
 3) is there an up to data set of install instructions for  Gromacs 2018
 and Nvidia 9.1 toolkit,  384.11 drivers ?
 
>>> No, there's nothing unusual about that, so the generic instructions apply.
>>> 
>>> Mark
>>> 
>>> 
 Regards
 Paul
 --
 Gromacs Users mailing list
 
 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!
 
 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.
>>> -- 
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 
>>>  before 
>>> posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 
>>> 
>>> 
>>> * For (un)subscribe requests visit
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>>>  or 
>>> send a mail to gmx-users-requ...@gromacs.org 
>>> .
> 
> -- 
> ==
> 
> 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 
> 
> ==
> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 
> 

Re: [gmx-users] Gromacs 2018 and GPU

[Justin Lemkul]

On 5/4/18 1:48 PM, paul buscemi wrote:

thank you for the prompt response.  I will check out the link.  Regarding 2)  
One can immediately determine if the GPU is/is  running since Gromacs tells you 
at the beginning - in my case - that the CPU’s being used and linux system 
monitor tells you that all CPU’s are running, - not to mention the fan speed, 
and nvidia-smi registers no GPU running

What I was asking was for the proper format for invoking the GPU .  I used
gmx mdrun -deffnm md_0_1 -nb gpu ##   this is from the lysozyme tutorial MD 
page
but this starts Gromacs using the CPU’s and was asking if this is a proper 
format for a single GPU.


With version 2018, you don't even need to use "-nb gpu," mdrun will 
automatically run on the GPU if it is detected properly. As Mark said, 
check your .log file for a full breakdown of how mdrun configured the 
simulation using the available hardware.


-Justin


thanks
Paul


On 4,May 2018, at 11:57 AM, Mark Abraham  wrote:

Hi,

On Fri, May 4, 2018 at 6:43 PM paul buscemi > wrote:



I’ve been struggling for a for several days to get Gromacs-2018 to use my
GPU.  I followed the INSTALL instructions ( several times ! ) that are
provided in the 2018 tarball

I know that the GPU ( GTX1080)  is installed properly in that it works
with Schrodinger and the Nvidia self tests.  Gromacs runs the  MD from the
University of Baltimore  lysozyme  example normally
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
<
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/>
but only on the 8 threads of the  CPU


The tutorial explicitly addresses this. See
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html
 




Make test  indicates that it sees the GPU, but

1)  is there a way to definitively determine if the make commands were run
properly or that Gromacs was installed properly with the GPU


To know that a simulation ran on the GPU, you must inspect the log file
that it wrote.



2) for a linux desktop system with one GPU,  a/the  proper command to run
the lysozyme .  I ask since there is indication that with one GPU  (0) it
will be dedicated to graphics.


If the display is sharing the GPU, then it shares the GPU (and performance
of either the display or the simulation might be affected). With only one
GPU, there's no option (unless your motherboard has a built-in GPU that
you'd prefer to use for the display).



3) is there an up to data set of install instructions for  Gromacs 2018
and Nvidia 9.1 toolkit,  384.11 drivers ?


No, there's nothing unusual about that, so the generic instructions apply.

Mark



Regards
Paul
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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] Gromacs 2018 and GPU

[paul buscemi]

thank you for the prompt response.  I will check out the link.  Regarding 2)  
One can immediately determine if the GPU is/is  running since Gromacs tells you 
at the beginning - in my case - that the CPU’s being used and linux system 
monitor tells you that all CPU’s are running, - not to mention the fan speed, 
and nvidia-smi registers no GPU running

What I was asking was for the proper format for invoking the GPU .  I used 
gmx mdrun -deffnm md_0_1 -nb gpu ##   this is from the lysozyme tutorial MD 
page
but this starts Gromacs using the CPU’s and was asking if this is a proper 
format for a single GPU.

thanks
Paul

> On 4,May 2018, at 11:57 AM, Mark Abraham  wrote:
> 
> Hi,
> 
> On Fri, May 4, 2018 at 6:43 PM paul buscemi  > wrote:
> 
>> 
>> 
>> I’ve been struggling for a for several days to get Gromacs-2018 to use my
>> GPU.  I followed the INSTALL instructions ( several times ! ) that are
>> provided in the 2018 tarball
>> 
>> I know that the GPU ( GTX1080)  is installed properly in that it works
>> with Schrodinger and the Nvidia self tests.  Gromacs runs the  MD from the
>> University of Baltimore  lysozyme  example normally
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
>> <
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/>
>> but only on the 8 threads of the  CPU
>> 
> 
> The tutorial explicitly addresses this. See
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html
>  
> 
> 
> 
>> Make test  indicates that it sees the GPU, but
>> 
>> 1)  is there a way to definitively determine if the make commands were run
>> properly or that Gromacs was installed properly with the GPU
>> 
> 
> To know that a simulation ran on the GPU, you must inspect the log file
> that it wrote.
> 
> 
>> 2) for a linux desktop system with one GPU,  a/the  proper command to run
>> the lysozyme .  I ask since there is indication that with one GPU  (0) it
>> will be dedicated to graphics.
>> 
> 
> If the display is sharing the GPU, then it shares the GPU (and performance
> of either the display or the simulation might be affected). With only one
> GPU, there's no option (unless your motherboard has a built-in GPU that
> you'd prefer to use for the display).
> 
> 
>> 3) is there an up to data set of install instructions for  Gromacs 2018
>> and Nvidia 9.1 toolkit,  384.11 drivers ?
>> 
> 
> No, there's nothing unusual about that, so the generic instructions apply.
> 
> Mark
> 
> 
>> 
>> Regards
>> Paul
>> --
>> 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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> 
> * 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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>  or send 
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> .

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Re: [gmx-users] Gromacs 2018 and GPU

[Mark Abraham]

Hi,

On Fri, May 4, 2018 at 6:43 PM paul buscemi  wrote:

>
>
> I’ve been struggling for a for several days to get Gromacs-2018 to use my
> GPU.  I followed the INSTALL instructions ( several times ! ) that are
> provided in the 2018 tarball
>
> I know that the GPU ( GTX1080)  is installed properly in that it works
> with Schrodinger and the Nvidia self tests.  Gromacs runs the  MD from the
> University of Baltimore  lysozyme  example normally
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
> <
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/>
> but only on the 8 threads of the  CPU
>

The tutorial explicitly addresses this. See
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html


> Make test  indicates that it sees the GPU, but
>
> 1)  is there a way to definitively determine if the make commands were run
> properly or that Gromacs was installed properly with the GPU
>

To know that a simulation ran on the GPU, you must inspect the log file
that it wrote.


> 2) for a linux desktop system with one GPU,  a/the  proper command to run
> the lysozyme .  I ask since there is indication that with one GPU  (0) it
> will be dedicated to graphics.
>

If the display is sharing the GPU, then it shares the GPU (and performance
of either the display or the simulation might be affected). With only one
GPU, there's no option (unless your motherboard has a built-in GPU that
you'd prefer to use for the display).


> 3) is there an up to data set of install instructions for  Gromacs 2018
> and Nvidia 9.1 toolkit,  384.11 drivers ?
>

No, there's nothing unusual about that, so the generic instructions apply.

Mark


>
> Regards
> Paul
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[gmx-users] Gromacs 2018 and GPU

[paul buscemi]

I’ve been struggling for a for several days to get Gromacs-2018 to use my GPU.  
I followed the INSTALL instructions ( several times ! ) that are provided in 
the 2018 tarball

I know that the GPU ( GTX1080)  is installed properly in that it works with 
Schrodinger and the Nvidia self tests.  Gromacs runs the  MD from the 
University of Baltimore  lysozyme  example normally  
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
 

  but only on the 8 threads of the  CPU

Make test  indicates that it sees the GPU, but 

1)  is there a way to definitively determine if the make commands were run 
properly or that Gromacs was installed properly with the GPU

2) for a linux desktop system with one GPU,  a/the  proper command to run the 
lysozyme .  I ask since there is indication that with one GPU  (0) it will be 
dedicated to graphics.


3) is there an up to data set of install instructions for  Gromacs 2018 and 
Nvidia 9.1 toolkit,  384.11 drivers ?

Regards
Paul
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Re: [gmx-users] Fluctuations in HII phase

[Mohsen Ramezanpour]

Thanks Justin! It sounds an interesting approach. I will give it a try.

Cheers,
Mohsen




On Fri, May 4, 2018 at 8:15 AM, Justin Lemkul  wrote:

>
>
> On 5/3/18 10:36 PM, Mohsen Ramezanpour wrote:
>
>> Hi Gromacs users,
>>
>> I have a cylinder composed of lipids with waters inside (HII phase).
>> This lipid tube fluctuates along the Z-axis.
>> That being said, if we slice the cylinder in the Z direction, the center
>> of
>> mass (COM) for each slice is moving around in the XY plane. You can
>> imagine
>> it as a 1D undulations in the Z direction.
>>
>> I want to quantitively show that some of these cylinders are more dynamics
>> than others in nature.
>>
>> Snapshots from the system are one of the solutions but can not be used for
>> quantitative comparisons between several systems with a different level of
>> undulations. It just shows these systems are bent.
>>
>> The average size of the system in the Z direction and its fluctuations
>> might be another naive quantity to be considered. If the Z size is fixed
>> and the system is behaving like a wave, this would not give what I want
>> either.
>>
>> So, I would like to know your opinion on what would be the best way to
>> show
>> such undulations in a quantitative way?
>>
>
> I would plot the x-y COM position as a function of some selection of atoms
> along z, and calculate the fluctuation in COM position about the mean. If
> the structure is indeed more dynamic, that slice should fluctuate more than
> another system that is more rigid. Think of it as the RMSF of the COM in
> the plane.
>
> -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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> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] Slowly changing the q and vdw interactions for free energy calculations

[Qasim Pars]

Hi,

Any comments on my questions?

> On 3 May 2018, at 19:48, Qasim Pars  wrote:
> 
> Dear users,
> 
> For the binding free energy calculations I would slowly first turn off the 
> coulomb interactions, and then the vdw interactions at only one production 
> step of 1 ns (not multiple simulations as in MBAR). My questions are:
> Can I do that with gromacs?
> I don't know whether the following settings are correct or not? 
> According to the following settings the simulation time between two lambda 
> states will be 100 ps, right? Or do I need to use delta-lamda?
> 
> free-energy = yes
> init-lambda = 0
> coul-lambdas = 0.0 0.1 0.2 0.5 1.0 1.0 1.0 1.0 1.0 1.0
> vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0
> sc-alpha = 0.5
> sc-power = 1
> sc-sigma = 0.3
> couple-moltype = ligand
> couple-lambda0 = vdw-q
> couple-lambda1 = none
> couple-intramol = no
> nstdhdl = 1
> 
> Any help will be appreciated.
> Thanks
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Re: [gmx-users] Fluctuations in HII phase

[Justin Lemkul]

On 5/3/18 10:36 PM, Mohsen Ramezanpour wrote:

Hi Gromacs users,

I have a cylinder composed of lipids with waters inside (HII phase).
This lipid tube fluctuates along the Z-axis.
That being said, if we slice the cylinder in the Z direction, the center of
mass (COM) for each slice is moving around in the XY plane. You can imagine
it as a 1D undulations in the Z direction.

I want to quantitively show that some of these cylinders are more dynamics
than others in nature.

Snapshots from the system are one of the solutions but can not be used for
quantitative comparisons between several systems with a different level of
undulations. It just shows these systems are bent.

The average size of the system in the Z direction and its fluctuations
might be another naive quantity to be considered. If the Z size is fixed
and the system is behaving like a wave, this would not give what I want
either.

So, I would like to know your opinion on what would be the best way to show
such undulations in a quantitative way?


I would plot the x-y COM position as a function of some selection of 
atoms along z, and calculate the fluctuation in COM position about the 
mean. If the structure is indeed more dynamic, that slice should 
fluctuate more than another system that is more rigid. Think of it as 
the RMSF of the COM in the plane.


-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] Charmm-Gui output to Gromacs

[Justin Lemkul]

On 5/4/18 5:35 AM, Mark Abraham wrote:

Hi,

Charmm-GUI writes GROMACS files natively, doesn't it?


It does. I haven't run the Glycan Reader directly but it is embedded as 
a component of the Quick MD Simulator, which gives all necessary GROMACS 
input files (coordinates, topology, and .mdp).


-Justin


Mark

On Fri, May 4, 2018 at 10:16 AM Frederic Schneider <
frederic.schnei...@tu-bs.de> wrote:


Hello everyone,

i would like to convert the topology files from the output of the
Charmm-Gui/Glycan Reader(.psf file) to the Gromacs format (.itp, .top).

Is there a preferred script or program to do this task?

Best regards,

Frederic

Frederic Schneider, M.Sc.
TU Braunschweig
Institut für Medizinische und
Pharmazeutische Chemie
Beethovenstraße 55
38106 Braunschweig
Tel.:+49 (0)5 31/ 391 84 51

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==

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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
http://www.thelemkullab.com

==

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Re: [gmx-users] Covarience matrix eps file atom interval set -reg

[Justin Lemkul]

On 5/4/18 10:01 AM, venkat wrote:

  Hi,
  I did  covar analysis  with option  xpma  for  1188  c-alpha atoms ,
followed by xpma file converted using xpm2ps , i got following image , here
need is to set or interval of  200 atoms. How can I do this ?   (i tried
with -do flag for modified .m2p file , not working for me )


http://manual.gromacs.org/documentation/current/user-guide/file-formats.html#m2p

Set x-major = 200 and y-major = 200

-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] Covarience matrix eps file atom interval set -reg

[venkat]

 Hi,
 I did  covar analysis  with option  xpma  for  1188  c-alpha atoms ,
followed by xpma file converted using xpm2ps , i got following image , here
need is to set or interval of  200 atoms. How can I do this ?   (i tried
with -do flag for modified .m2p file , not working for me )

kindly provide suggestion

thanks you in advance

click view the image

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Re: [gmx-users] Charmm-Gui output to Gromacs

[Mark Abraham]

Hi,

Charmm-GUI writes GROMACS files natively, doesn't it?

Mark

On Fri, May 4, 2018 at 10:16 AM Frederic Schneider <
frederic.schnei...@tu-bs.de> wrote:

> Hello everyone,
>
> i would like to convert the topology files from the output of the
> Charmm-Gui/Glycan Reader(.psf file) to the Gromacs format (.itp, .top).
>
> Is there a preferred script or program to do this task?
>
> Best regards,
>
> Frederic
>
> Frederic Schneider, M.Sc.
> TU Braunschweig
> Institut für Medizinische und
> Pharmazeutische Chemie
> Beethovenstraße 55
> 38106 Braunschweig
> Tel.:+49 (0)5 31/ 391 84 51
>
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Re: [gmx-users] REMD temperature_space

[Mark Abraham]

Hi,

Unfortunately nobody has implemented demux for the energy files. You could
consider contributing a modification of demux.pl :-)

Mark

On Fri, May 4, 2018 at 8:42 AM Sundari  wrote:

> Hello Guys,
>
> Kindly suggest me something about my doubt.
>
> On Thu, May 3, 2018 at 5:19 PM, Sundari  wrote:
>
> > Hello,
> >
> > I got the continuous trajectories by using demux. But now I am confused
> in
> > getting potential energy distribution of a single replica (similarly time
> > evolution of a replica (say replica_1) in temperature space).
> > I used edr file of original production data files, but I am not getting
> > what I want. I am attaching the temp.xvg file of one replica (say T= 315K
> > replica)
> >
> > Thank You..
> >
> > On Thu, May 3, 2018 at 5:02 PM, Mark Abraham 
> > wrote:
> >
> >> Hi,
> >>
> >> It sounds like you just want to use the original data, which you had
> >> before
> >> you ran the demux script.
> >>
> >> Mark
> >>
> >> On Thu, May 3, 2018 at 1:28 PM Sundari  wrote:
> >>
> >> > Dear gromacs users,
> >> >
> >> > can anyone please suggest me that how we  get the time evolution of a
> >> > replica (say replica_1) in temperature space and time courses of
> >> potential
> >> > energy of each replica(  one way is md.edr file??)
> >> > As according to GROMACS tutorial, I used demux.pl script and got two
> >> files
> >> > replica_index.xvg and replica_temp.xvg.  But I want to analyse a
> single
> >> > replica trajectory in all temperatures ( temp. on y-axis)
> >> >
> >> >
> >> > Thank you in advance..
> >> >
> >> > Sundari
> >> > --
> >> > 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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> >
> >
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[gmx-users] Charmm-Gui output to Gromacs

[Frederic Schneider]

Hello everyone,

i would like to convert the topology files from the output of the 
Charmm-Gui/Glycan Reader(.psf file) to the Gromacs format (.itp, .top).


Is there a preferred script or program to do this task?

Best regards,

Frederic

Frederic Schneider, M.Sc.
TU Braunschweig
Institut für Medizinische und
Pharmazeutische Chemie
Beethovenstraße 55
38106 Braunschweig
Tel.:+49 (0)5 31/ 391 84 51

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Re: [gmx-users] REMD temperature_space

[Sundari]

Hello Guys,

Kindly suggest me something about my doubt.

On Thu, May 3, 2018 at 5:19 PM, Sundari  wrote:

> Hello,
>
> I got the continuous trajectories by using demux. But now I am confused in
> getting potential energy distribution of a single replica (similarly time
> evolution of a replica (say replica_1) in temperature space).
> I used edr file of original production data files, but I am not getting
> what I want. I am attaching the temp.xvg file of one replica (say T= 315K
> replica)
>
> Thank You..
>
> On Thu, May 3, 2018 at 5:02 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> It sounds like you just want to use the original data, which you had
>> before
>> you ran the demux script.
>>
>> Mark
>>
>> On Thu, May 3, 2018 at 1:28 PM Sundari  wrote:
>>
>> > Dear gromacs users,
>> >
>> > can anyone please suggest me that how we  get the time evolution of a
>> > replica (say replica_1) in temperature space and time courses of
>> potential
>> > energy of each replica(  one way is md.edr file??)
>> > As according to GROMACS tutorial, I used demux.pl script and got two
>> files
>> > replica_index.xvg and replica_temp.xvg.  But I want to analyse a single
>> > replica trajectory in all temperatures ( temp. on y-axis)
>> >
>> >
>> > Thank you in advance..
>> >
>> > Sundari
>> > --
>> > 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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>> > 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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>>
>> * Please search the archive at http://www.gromacs.org/Support
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>>
>
>
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