[gmx-users] saving trajectories at a logarithmic frequency

[Jagannath Mondal]

Dear all
  Is it possible to save trajectories in gromacs not at constant frequency
but at a logarithmic frequency?
Jagannath
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[gmx-users] Any update on constant pH simulation?

[Jagannath Mondal]

Dear Gromacs users and developers
  Is there any new update on implementation of constant pH simulations on
recent gromacs version?
I am aware of the gromacs faq
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
But I wanted to check if there is any update on this ?
Jagannath
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[gmx-users] number of water molecules along z

[Jagannath Mondal]

Dear Gromacs-users

  I need to compute the time profile of number of water away from a
membrane center along z direction. However trjorder -nshell -r 0.6 will
give me the number of waters along radial direction.
  there is an option in trjorder -z . but that just orders molecule along
z. but does not let one calculate water number along z at a cutoff distance.
Is there any other ways of getting it?
Jagannath
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Re: [gmx-users] query on performance of GTX 1080 in gromacs

[Jagannath Mondal]

Hi Mark
  Sorry to ask again, but is there an update on the feasibility of gromacs
in gtx1080 ?
Jagannath

On Fri, May 27, 2016 at 10:36 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Yes, we expect it to work, but we haven't tried it yet. NVIDIA didn't
> manage to give us any early access, in practice. We have some cards, but
> perhaps no actual run until early next week.
>
> Mark
>
> On Fri, 27 May 2016 18:22 Jagannath Mondal <jmondal.bac...@gmail.com>
> wrote:
>
> > Dear Gromacs users
> >
> >   I just wanted to check whether latest GPU of NVIDIA GTX 1080 has been
> > tested by any one for its compatibility/performance with gromacs.
> >
> > I have used GTX 980 Ti and have found it compatible with gromacs with a
> > significant performance boosting. I wanted to check if the latest release
> > of NVIDIA GTX 1080 will work with Gromacs.
> >
> > I will appreciate your feedback.
> >
> > Jagannath
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] query on performance of GTX 1080 in gromacs

[jagannath mondal]

Hi Mark
  Sorry to ask again, but is there an update on the feasibility of gromacs
in gtx1080 ?
Jagannath

On Fri, May 27, 2016 at 10:36 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Yes, we expect it to work, but we haven't tried it yet. NVIDIA didn't
> manage to give us any early access, in practice. We have some cards, but
> perhaps no actual run until early next week.
>
> Mark
>
> On Fri, 27 May 2016 18:22 Jagannath Mondal <jmondal.bac...@gmail.com>
> wrote:
>
> > Dear Gromacs users
> >
> >   I just wanted to check whether latest GPU of NVIDIA GTX 1080 has been
> > tested by any one for its compatibility/performance with gromacs.
> >
> > I have used GTX 980 Ti and have found it compatible with gromacs with a
> > significant performance boosting. I wanted to check if the latest release
> > of NVIDIA GTX 1080 will work with Gromacs.
> >
> > I will appreciate your feedback.
> >
> > Jagannath
> > --
> > 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] problem installing gromacs in ubuntu

[Jagannath Mondal]

Hi
  My installation of gromacs_5.0.6 is not working at 'make' stage in
ubuntu. The same machine had no problem in installing the same version
earlier.
I am having following issues near the completion of 'make' stage:
Any help will be appreciated.

 [100%] *Linking CXX executable ../../bin/template*

/usr/lib/libf77blas.so.3gf: undefined reference to
`_gfortran_transfer_integer_write@GFORTRAN_1.4'

/usr/lib/libf77blas.so.3gf: undefined reference to
`_gfortran_transfer_character_write@GFORTRAN_1.4'

collect2: error: ld returned 1 exit status

make[2]: *** [bin/gmx_cyl] Error 1

make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2

make[1]: *** Waiting for unfinished jobs

/usr/lib/libf77blas.so.3gf: undefined reference to
`_gfortran_transfer_integer_write@GFORTRAN_1.4'

/usr/lib/libf77blas.so.3gf: undefined reference to
`_gfortran_transfer_character_write@GFORTRAN_1.4'

collect2: error: ld returned 1 exit status

make[2]: *** [bin/template] Error 1

make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2

make: *** [all] Error 2


The command I used:

cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_INSTALL_PREFIX=/home/jmondal/UTIL/GROMACS_5.0.6
-DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_cyl -DGMX_LIBS_SUFFIX=_cyl
-DGMX_GPU=off


make
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Re: [gmx-users] query on performance of GTX 1080 in gromacs

[Jagannath Mondal]

Dear Mark
  Did you have a chance to test gromacs with GTX 1080? Can you please let
us know if it is compatible and working well.
Jagannath

On Sat, May 28, 2016 at 2:36 PM, Jagannath Mondal <jmondal.bac...@gmail.com>
wrote:

> Dear Mark
>
>I will appreciate if you share your experience, once you tested with
> GTX 1080. I can wait for your response.
>
> Jagannath
>
>
> On Fri, May 27, 2016 at 10:36 PM, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
>> Hi,
>>
>> Yes, we expect it to work, but we haven't tried it yet. NVIDIA didn't
>> manage to give us any early access, in practice. We have some cards, but
>> perhaps no actual run until early next week.
>>
>> Mark
>>
>> On Fri, 27 May 2016 18:22 Jagannath Mondal <jmondal.bac...@gmail.com>
>> wrote:
>>
>> > Dear Gromacs users
>> >
>> >   I just wanted to check whether latest GPU of NVIDIA GTX 1080 has been
>> > tested by any one for its compatibility/performance with gromacs.
>> >
>> > I have used GTX 980 Ti and have found it compatible with gromacs with a
>> > significant performance boosting. I wanted to check if the latest
>> release
>> > of NVIDIA GTX 1080 will work with Gromacs.
>> >
>> > I will appreciate your feedback.
>> >
>> > Jagannath
>> > --
>> > 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!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] query on performance of GTX 1080 in gromacs

[Jagannath Mondal]

Dear Mark

   I will appreciate if you share your experience, once you tested with GTX
1080. I can wait for your response.

Jagannath


On Fri, May 27, 2016 at 10:36 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Yes, we expect it to work, but we haven't tried it yet. NVIDIA didn't
> manage to give us any early access, in practice. We have some cards, but
> perhaps no actual run until early next week.
>
> Mark
>
> On Fri, 27 May 2016 18:22 Jagannath Mondal <jmondal.bac...@gmail.com>
> wrote:
>
> > Dear Gromacs users
> >
> >   I just wanted to check whether latest GPU of NVIDIA GTX 1080 has been
> > tested by any one for its compatibility/performance with gromacs.
> >
> > I have used GTX 980 Ti and have found it compatible with gromacs with a
> > significant performance boosting. I wanted to check if the latest release
> > of NVIDIA GTX 1080 will work with Gromacs.
> >
> > I will appreciate your feedback.
> >
> > Jagannath
> > --
> > 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
>
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[gmx-users] query on performance of GTX 1080 in gromacs

[Jagannath Mondal]

Dear Gromacs users

  I just wanted to check whether latest GPU of NVIDIA GTX 1080 has been
tested by any one for its compatibility/performance with gromacs.

I have used GTX 980 Ti and have found it compatible with gromacs with a
significant performance boosting. I wanted to check if the latest release
of NVIDIA GTX 1080 will work with Gromacs.

I will appreciate your feedback.

Jagannath
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Re: [gmx-users] Combining various Flat-bottomed Potentials

[Jagannath Mondal]

Hi
  I am also interested in the issue of using a  flat-bottomed restraint,
for a spherocylinder.
 However, I am not sure whether the current gromacs settings of even a
linear combination of a sphere and cylinder can help here to generate a
spherocylinder.

If we put the spherical and cylindrical restraint on the same particle
(under the [position restraints] flag as Justin and Chris has suggested ),
the particle will be either be in a spherical confinement or in a
cylindrical confinement .  But for a spherocylinder, we need two
hemispheres which are capped on the two ends of a cylinder.
Hence, for a spherocylindrical restraint, what is needed here is a
restraint which will restrain the particle on going out when the z
coordinate of the particle exceeds the diameter of the cylinder AND the
sqrt(x**2+y**2) of the particle exceeds the length of the cylinder.
I am wondering whether this is possible within the current gromacs
implentation.
If it is not, I was interested in editing the source code relevant for flat
bottomed potential, to implement it for a spherocylinder. Is the following
path within gromacs directory right place to make the changes ?
  gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c

Any suggestions will be welcome.
Thanks

On Wed, May 25, 2016 at 2:22 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Thanks for the clarification Justin.
>
> Those interested in using these potentials (as I was) should be careful as
> I think that at lease some forms are broken when using domain decomposition:
> http://redmine.gromacs.org/issues/1969
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul 
> Sent: 24 May 2016 12:33:54
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Combining various Flat-bottomed Potentials
>
> On 5/24/16 12:30 PM, Christopher Neale wrote:
> > I doubt it. The flat-bottom potential in the pull-code is not really the
> standard definition of a flat-bottom potential. In my opinion, a
> flat-bottom potential has a low, and a high defined value and then the
> restraint increases harmonically above high and below low with no penalty
> between low and high set values. However, the gromacs 5.1.2 flat-bottom
> potential is simply a regular potential where the forces are set to zero
> below the central set point and there is a harmonic above the central set
> point. I'd call this a half-harmonic rather than a flat-bottom potential.
> Luckily, the code is quite simple to modify to get a proper flat-bottom
> potential, which you could use to get your cylinder.
> >
> > You want to modify src/gromacs/pulling/pull.cpp around line 1129 and
> remove the code:
> >
> >  if (pcrd->params.eType == epullFLATBOTTOM && dev < 0)
> > {
> > dev = 0;
> > }
> >
> > And replace it with:
> >
> >if (pcrd->params.eType == epullFLATBOTTOM)
> > {
> > if (dev > -1 && dev <1){
> >   dev = 0;
> > } else {
> >   if (dev >0){
> > dev-=1;
> >   }else {
> > dev+=1;
> >   }
> > }
> > }
> >
> > That will give you a flat-bottom width of 2.0 nm (1 nm on each side).
> This is the quick and dirty approach where you just hard-code your
> potential flat-bottom width then compile it like that. You will need to
> change the "1" in four places if you want a different width.
> >
>
> If I understand the OP correctly, this isn't a matter of using the pull
> code,
> rather simultaneously using flat-bottom options in [position_restraints].
> It
> should be possible to simply combine the available options to whatever the
> user
> desires.  Several people have asked the same question in recent days, yet
> it
> doesn't seem like anyone's actually *tried* to do it yet.  That would be a
> much
> more useful effort :)
>
> -Justin
>
> > Obviously test it also prior to production.
> >
> > Chris.
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Srajan
> Jain 
> > Sent: 24 May 2016 05:13:17
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Combining various Flat-bottomed Potentials
> >
> > Dear Gromacs users,
> >
> > I want to impose a sphero-cylinderical position restraint, using
> > flat-bottomed potentials, for a simulation.
> >
> > The manual mentions that we can combine the existing three flat-bottomed
> > potentials, like a cylinder with two layers to get a disk.
> >
> > So, can this feature be used to generate a sphero-cylinder?
> >
> > Thank you in advance.
> > --
> > Gromacs Users mailing list
> >
> > * Please 

Re: [gmx-users] Combining various Flat-bottomed Potentials

[jagannath mondal]

Hi
  I am also interested in the issue of using a  flat-bottomed restraint,
for a spherocylinder.
 However, I am not sure whether the current gromacs settings of even a
linear combination of a sphere and cylinder can help here to generate a
spherocylinder.

If we put the spherical and cylindrical restraint on the same particle
(under the [position restraints] flag as Justin and Chris has suggested ),
the particle will be either be in a spherical confinement or in a
cylindrical confinement .  But for a spherocylinder, we need two
hemispheres which are capped on the two ends of a cylinder.
Hence, for a spherocylindrical restraint, what is needed here is a
restraint which will restrain the particle on going out when the z
coordinate of the particle exceeds the diameter of the cylinder AND the
sqrt(x**2+y**2) of the particle exceeds the length of the cylinder.
I am wondering whether this is possible within the current gromacs
implentation.
If it is not, I was interested in editing the source code relevant for flat
bottomed potential, to implement it for a spherocylinder. Is the following
path within gromacs directory right place to make the changes ?
  gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c

Any suggestions will be welcome.
Thanks
Jagannath

On Wed, May 25, 2016 at 2:22 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Thanks for the clarification Justin.
>
> Those interested in using these potentials (as I was) should be careful as
> I think that at lease some forms are broken when using domain decomposition:
> http://redmine.gromacs.org/issues/1969
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul 
> Sent: 24 May 2016 12:33:54
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Combining various Flat-bottomed Potentials
>
> On 5/24/16 12:30 PM, Christopher Neale wrote:
> > I doubt it. The flat-bottom potential in the pull-code is not really the
> standard definition of a flat-bottom potential. In my opinion, a
> flat-bottom potential has a low, and a high defined value and then the
> restraint increases harmonically above high and below low with no penalty
> between low and high set values. However, the gromacs 5.1.2 flat-bottom
> potential is simply a regular potential where the forces are set to zero
> below the central set point and there is a harmonic above the central set
> point. I'd call this a half-harmonic rather than a flat-bottom potential.
> Luckily, the code is quite simple to modify to get a proper flat-bottom
> potential, which you could use to get your cylinder.
> >
> > You want to modify src/gromacs/pulling/pull.cpp around line 1129 and
> remove the code:
> >
> >  if (pcrd->params.eType == epullFLATBOTTOM && dev < 0)
> > {
> > dev = 0;
> > }
> >
> > And replace it with:
> >
> >if (pcrd->params.eType == epullFLATBOTTOM)
> > {
> > if (dev > -1 && dev <1){
> >   dev = 0;
> > } else {
> >   if (dev >0){
> > dev-=1;
> >   }else {
> > dev+=1;
> >   }
> > }
> > }
> >
> > That will give you a flat-bottom width of 2.0 nm (1 nm on each side).
> This is the quick and dirty approach where you just hard-code your
> potential flat-bottom width then compile it like that. You will need to
> change the "1" in four places if you want a different width.
> >
>
> If I understand the OP correctly, this isn't a matter of using the pull
> code,
> rather simultaneously using flat-bottom options in [position_restraints].
> It
> should be possible to simply combine the available options to whatever the
> user
> desires.  Several people have asked the same question in recent days, yet
> it
> doesn't seem like anyone's actually *tried* to do it yet.  That would be a
> much
> more useful effort :)
>
> -Justin
>
> > Obviously test it also prior to production.
> >
> > Chris.
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Srajan
> Jain 
> > Sent: 24 May 2016 05:13:17
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Combining various Flat-bottomed Potentials
> >
> > Dear Gromacs users,
> >
> > I want to impose a sphero-cylinderical position restraint, using
> > flat-bottomed potentials, for a simulation.
> >
> > The manual mentions that we can combine the existing three flat-bottomed
> > potentials, like a cylinder with two layers to get a disk.
> >
> > So, can this feature be used to generate a sphero-cylinder?
> >
> > Thank you in advance.
> > --
> > Gromacs Users mailing list
> >
> 

[gmx-users] query on implementation details of flat-bottomed potential

[Jagannath Mondal]

Hi
  I have to impose a  spherocylindrical confinement on the particles I am
 currently performing simulation with.
For that I will appreciate your feedback/comments regarding two of my plans:

1.  I was mainly looking at flat-bottomed potential option within gromacs
to see if it can be used to implement a spherocylindrical confinement.
However, the current implementation of gromacs works with either for sphere
or cylinder. But it is  not implemented for spherocylinder. I was wondering
whether it is possible to create a combination of both of the existing
flatbottomed potential to obtain a spherocylindrical potential.

 If the current gromacs implementation does not allow us to create a
spherocylindrical flat-bottomed potential, can someone point out the
location of relevant source code in gromacs directory where the
flat-bottomed potential is implemented ? I could then modify the source
code for a spherocylindrical geometry.

2. I was also thinking of alternative way of incorporating
spherocylindrical confinement by adding a table potential. But my question
is that one needs to define an energy group which will be interacting by
this table potential. But the spherocylindrical geometry does not have any
particle in boundary. In that case, how  can one proceed?

Your response will be appreciated.
Jagannath
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Re: [gmx-users] How to create a spherocylindrical wall

[Jagannath Mondal]

Hi
  This dates back to an old query on using restraints to create a
spherocylindricalconfinement.

  a) Based on previous suggestions, we were exploring the options of
flatbottomed potential.
   However, it has three options only: sphere, cylinder and layer. We
wanted to create a combination of cylinder and (hemi)sphere to make a
 hollow spherocylinder. But we do not find how to make the hemisphere using
flatbottomed potential.
  Also, we wanted to have the centers of cylinder and sphere in  different
locations. However, we are not sure within the current gromacs
implementation, how we can have two different centers for flat-bottomed
restraints.

b) In worse case scenario, we were thinking of modifying the source code of
gromacs flat-bottomed restraints to have the option of
spherocylindrical restraints.
In that case, can some one point out the relevant locations of source code
for flat-bottomed potential withing gromacs 5.x installation directory?


On Sat, Sep 12, 2015 at 7:52 AM, Barnett, James W <jbarn...@tulane.edu>
wrote:

> On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote:
> > Hi
> >   I would like to perform a simulation ( without any periodic
> > boundary
> > condition) where I need to have a wall of spherocylindrical geometry.
> > In
> > other words the particles will be confined inside a spherocylinder.
> >
> >  Is there any good suggestion on how to achieve that in gromacs?
> >
> > 1) One option I thought of achieving that is by having a
> > spherocylindrical
> > wall potential.  Is there a way of putting the wall potential in the
> > form
> > of a table-potential ? (Not sure cylinder option in gromacs umbrella
> > sampling  not going to be helpful).
>
> This might be do-able and would not require a table potential. Check
> out flat-bottom restraints in section 4.3.2 in the reference (PDF)
> manual.
>
> >
> > 2)  Or,should I put a bunch of hard sphere which constitute the
> > spherocylindrical boundary so that the particles inside the
> > spherocylinder
> > will have a repulsive interaction each time they come towards the
> > boundary ?
>
> I'm not sure how you would implement this in a simple way with GROMACS.
>
>
> --
> James “Wes” Barnett, Ph.D. Candidate
> Louisiana Board of Regents Fellow
>
> Chemical and Biomolecular Engineering
> Tulane University
> 341-B Lindy Boggs Center for Energy and Biotechnology
> 6823 St. Charles Ave
> New Orleans, Louisiana 70118-5674
> jbarn...@tulane.ed
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Re: [gmx-users] How to create a spherocylindrical wall

[jagannath mondal]

Hi
  This dates back to an old query on using restraints to create a
spherocylindrical confinement.

  a) Based on previous suggestions, we were exploring the options of
flatbottomed potential.
   However, it has three options only: sphere, cylinder and layer. We
wanted to create a combination of cylinder and (hemi)sphere to make a
 hollow spherocylinder. But we do not find how to make the hemisphere using
flatbottomed potential.
  Also, we wanted to have the centers of cylinder and sphere in  different
locations. However, we are not sure within the current gromacs
implementation, how we can have two different centers for flat-bottomed
restraints.

b) In worse case scenario, we were thinking of modifying the source code of
gromacs flat-bottomed restraints to have the option of spherocylindrical
restraints. In that case, can some one point out the relevant locations of
source code for flat-bottomed potential withing gromacs 5.x installation
directory?

Thanks
Jagannath

On Sat, Sep 12, 2015 at 7:52 AM, Barnett, James W <jbarn...@tulane.edu>
wrote:

> On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote:
> > Hi
> >   I would like to perform a simulation ( without any periodic
> > boundary
> > condition) where I need to have a wall of spherocylindrical geometry.
> > In
> > other words the particles will be confined inside a spherocylinder.
> >
> >  Is there any good suggestion on how to achieve that in gromacs?
> >
> > 1) One option I thought of achieving that is by having a
> > spherocylindrical
> > wall potential.  Is there a way of putting the wall potential in the
> > form
> > of a table-potential ? (Not sure cylinder option in gromacs umbrella
> > sampling  not going to be helpful).
>
> This might be do-able and would not require a table potential. Check
> out flat-bottom restraints in section 4.3.2 in the reference (PDF)
> manual.
>
> >
> > 2)  Or,should I put a bunch of hard sphere which constitute the
> > spherocylindrical boundary so that the particles inside the
> > spherocylinder
> > will have a repulsive interaction each time they come towards the
> > boundary ?
>
> I'm not sure how you would implement this in a simple way with GROMACS.
>
>
> --
> James “Wes” Barnett, Ph.D. Candidate
> Louisiana Board of Regents Fellow
>
> Chemical and Biomolecular Engineering
> Tulane University
> 341-B Lindy Boggs Center for Energy and Biotechnology
> 6823 St. Charles Ave
> New Orleans, Louisiana 70118-5674
> jbarn...@tulane.ed
> --
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[gmx-users] color-coding molecule location at different time frame

[Jagannath Mondal]

Dear gromacs-users
  I have a system of protein-ligand system.  I would like to use different
color for ligand location at different time-frame. The final goal is to
have a snapshot where ligand location of all time frame are color-coded
using a color-gradient ( for example : red at short time and blue at long
time). How can I achieve that ?
Thanks
Jagannath
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Re: [gmx-users] gpu-performance reduces during FEP calculation

[jagannath mondal]

Hi
  It is a small ligand decoupling from its native protein and there are
orientational restraints near high decoupled region.
I am using gcc and gfortran compilers .
Jagannath

On Tue, Mar 15, 2016 at 6:54 PM, Szilárd Páll <pall.szil...@gmail.com>
wrote:

> No, the free energy kernels run on the CPU. This large change must mean
> that you have a relatively large fraction of the system participating in
> perturbed interactions.
>
> What compiler are you using? The free energy kernel is a bit "sensitive"
> (to put it mildly) and I do remember seeing much better performance with
> some compilers than others.
>
> --
> Szilárd
>
> On Tue, Mar 15, 2016 at 2:18 PM, jagannath mondal <jm3...@columbia.edu>
> wrote:
>
> > Dear Gromacs users
> >   I am trying to perform Free energy peturbation calculation in presence
> of
> > distance, angle and dihedral-restraint for a protein-ligand system.
> > However, I am finding, on turning on the FEP calculation, the performance
> > of gromacs5.1.1. in a gpu-based workstation significantly gets reduced.
> the
> > gpu/cpu ratio reduces from 1 to 0.234 on turning on FEP module. I was
> > wondering whether FEP-module is still not using gpu-based optimization.
> > Jagannath
> > --
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[gmx-users] gpu-performance reduces during FEP calculation

[jagannath mondal]

Dear Gromacs users
  I am trying to perform Free energy peturbation calculation in presence of
distance, angle and dihedral-restraint for a protein-ligand system.
However, I am finding, on turning on the FEP calculation, the performance
of gromacs5.1.1. in a gpu-based workstation significantly gets reduced. the
gpu/cpu ratio reduces from 1 to 0.234 on turning on FEP module. I was
wondering whether FEP-module is still not using gpu-based optimization.
Jagannath
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Re: [gmx-users] query on plotting dynamical quantity

[jagannath mondal]

Hi Tsjerk
  Thanks for your suggestion on putting the parameters in bfactor column of
pdb. However, for this, the file format has to be a pdb format. However, if
I have a trajectory ( in xtc format) and each frame's 'bfactor' values are
getting updated, then do I need to convert entire xtc files into pdb files
for visualization?
Jagannath


On Tue, Mar 8, 2016 at 12:43 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:

> Hi Jagannath,
>
> Convert the file to PDB format and write the values to the b-factor field.
> Most visualization programs can color by b-value.
>
> Cheers,
>
> Tsjerk
> On Mar 8, 2016 06:50, "Jagannath Mondal" <jmondal.bac...@gmail.com> wrote:
>
> > Dear gromacs-users
> >
> >   I am sorry to write you a visualization-related query. I hope you can
> > help.
> >
> > My query is: How can I visualize a trajectory file ( example in vmd)
> where
> > I have an extra 4th column ( apart from x y z which are first 3 columns)
> > which has a dynamically changing variable for each particles ? The plan
> is
> > to color gradient the atoms using the values of   4th column.
> >
> >
> > Is there a way to do it. I am sorry again to write you off the list.
> >  Here is an excerpt from first few lines:
> > Jagannath
> >
> >219GLN  C  186.961000 4.468000 3.7760001.678980
> >
> > 220LEU  C  376.753000 4.257000 3.98  6.526284
> >
> > 221THR  C  516.618000 4.023000 4.151000  11.323132
> >
> > 222ALA  C  616.565000 3.742000 4.306000  26.957896
> >
> > 223ALA  C  716.409000 3.464000 4.313000  52.708403
> >
> > 224GLN  C  886.213000 3.54 4.528000
> > --
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[gmx-users] query on plotting dynamical quantity

[Jagannath Mondal]

Dear gromacs-users

  I am sorry to write you a visualization-related query. I hope you can
help.

My query is: How can I visualize a trajectory file ( example in vmd)  where
I have an extra 4th column ( apart from x y z which are first 3 columns)
which has a dynamically changing variable for each particles ? The plan is
to color gradient the atoms using the values of   4th column.


Is there a way to do it. I am sorry again to write you off the list.
 Here is an excerpt from first few lines:
Jagannath

   219GLN  C  186.961000 4.468000 3.7760001.678980

220LEU  C  376.753000 4.257000 3.98  6.526284

221THR  C  516.618000 4.023000 4.151000  11.323132

222ALA  C  616.565000 3.742000 4.306000  26.957896

223ALA  C  716.409000 3.464000 4.313000  52.708403

224GLN  C  886.213000 3.54 4.528000
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Re: [gmx-users] generating martini-version of lipids

[jagannath mondal]

Hi Tsjerk

   I have created a "dppg.charmm36.map" file using the template provided by
popg and dppc mapping . Then I had put 'dppg.charmm36,map'  file in the
Mapping folder.
 However, If I want to  do forward transformation i.e. going from charmm36
to martini , issuing the following command, it crashes:
  ./backward.py -f 1lip.gro -o 1lip_martini.gro -from charmm36 -to martini

"Error reading charmm36 to martini mapping for DPPG (file:
/home/jmondal/CG_MARTINI_Backup/MARTINI_BETA_PEPTIDE_REVISITED/New_martini_tools/BACKWARD/Mapping/leu.charmm36.map).
Residues defined for transformation from charmm36 to martini:
['POPC', 'ILE', 'POPG', 'GLN', 'POPS', 'GLY', 'GLU', 'CYS', 'ASP', 'POPE',
'LYS', 'PRO', 'CHOL', 'ASN', 'VAL', 'DPPC', 'DOPC', 'THR', 'HIS', 'TRP',
'SER', 'PHE', 'ALA', 'MET', 'LEU', 'ARG', 'TYR']
Traceback (most recent call last):
  File "./backward.py", line 821, in 
raise ValueError, "Unknown residue: %s\n"%resn
ValueError: Unknown residue: DPPG "


However, I try the backword mapping option, it at least tries something
i.e. at least can locate dppg lipids. But, it 'bails out' due to some other
issue.
I think, for forward mapping I am missing out something.
Below I paste first few lines of my dppg.charmm36.map file that I created.
If you want, I can send you the files by email. But, I think all the
mapping files that are present in Mapping folder are meant for backward
mapping. Can you please check?

[ molecule ]
DPPG

[ martini ]
GL0 PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B D3B C4B C5B

[ mapping ]
charmm36

[ atoms ]
1   C13 GL0
2   H13AGL0
3   H13BGL0
4   OC3 GL0
5   HO3 GL0
6   C12 GL0 GL0 GL0 PO4
7   H12AGL0
8   OC2 GL0


On Mon, Feb 29, 2016 at 10:10 PM, Tsjerk Wassenaar <tsje...@gmail.com>
wrote:

> Hi Jagannath,
>
> Backward actually can do both. For conversion of a Gromos system use
>
> backward.py -from gromos -to martini
>
> Hope it helps,
>
> Tsjerk
>
>
> On Mon, Feb 29, 2016 at 11:20 AM, Jagannath Mondal <
> jmondal.bac...@gmail.com
> > wrote:
>
> > Dear Gromacs/Martini-users
> >
> > I wanted to transform a snapshot of my atomistic DPPG/water bilayer to
> the
> > Martini coarse-grained format. However, I found martinize.py script  does
> > not transform lipid or waters to coarse-grained counterpart.It only works
> > for protein. So, Is there any particular way I can generate the CG
> version
> > of my atomistic DPPG/water bilayer ?
> >
> > I guess backward scripts does the reverse of what I am trying to achieve.
> > So, if you can suggest a way to generate a coarse-grained pdb files of
> the
> > atomistic lipid bilayer/water, that will be very helpful.
> >
> > Jagannath
> > --
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> >
>
>
>
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Re: [gmx-users] generating martini-version of lipids

[jagannath mondal]

Hi Tsjerk
  Thanks for your response. I was mainly looking for converting a dppg
bilayer in charm36 format into a coarse-grained one. However, the "Mapping"
folder does not have any mapping for dppg lipids. Is there any specific
suggestion regarding this?
Jagannath

On Mon, Feb 29, 2016 at 10:10 PM, Tsjerk Wassenaar <tsje...@gmail.com>
wrote:

> Hi Jagannath,
>
> Backward actually can do both. For conversion of a Gromos system use
>
> backward.py -from gromos -to martini
>
> Hope it helps,
>
> Tsjerk
>
>
> On Mon, Feb 29, 2016 at 11:20 AM, Jagannath Mondal <
> jmondal.bac...@gmail.com
> > wrote:
>
> > Dear Gromacs/Martini-users
> >
> > I wanted to transform a snapshot of my atomistic DPPG/water bilayer to
> the
> > Martini coarse-grained format. However, I found martinize.py script  does
> > not transform lipid or waters to coarse-grained counterpart.It only works
> > for protein. So, Is there any particular way I can generate the CG
> version
> > of my atomistic DPPG/water bilayer ?
> >
> > I guess backward scripts does the reverse of what I am trying to achieve.
> > So, if you can suggest a way to generate a coarse-grained pdb files of
> the
> > atomistic lipid bilayer/water, that will be very helpful.
> >
> > Jagannath
> > --
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> >
>
>
>
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Re: [gmx-users] Coarse Grain using martinize.py

[Jagannath Mondal]

Dear Tsjerk
  I had a similar question. I guess insane.py script is supposed to build a
coarse-grained membrane/solvent system from scratch. But, if I already have
a particular existing atomistic configuration of lipid/water system along
with some proteins ( which I had obtained by performing an atomistic
simulation), how do I generate a coarse-grained martini counter-part of
that specific atomistic snapshot ?

Your suggestion will be very helpful.

On Sat, Feb 27, 2016 at 3:29 AM, Tsjerk Wassenaar  wrote:

> Hi Ali,
>
> The current version of martinize is for coarse graining proteins and
> there's a version for nucleic acids. Lipids are not supported yet. These
> you could forward map with the program backward, but why the hassle as you
> can also directly build the coarse grain membrane/solvent system with
> insane (http://www.cgmartini.nl/index.php/downloads/tools/239-insane).
>
> Hope it helps,
>
> Tsjerk
> On Feb 26, 2016 22:36,  wrote:
>
>
>
> Dear all
> I want to simulate a system of 128 DPPC with 3655 water molecule which its
> .pdb file is available on professor tielman website. I want to Coarse
> grain it but apparently at first i should turn the pdb file into
> appropriate type for using with martini. I understood, I should use marti
> ize.py to convert the pdb but I dont know how. Also the tutorial wasnt
> helpful. Could anyone give me the direct command to do this ?
> best regards
> Ali
> ==
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
> Department of Mechanical Engineering
> Sharif University of Technology, Tehran, Iran
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Re: [gmx-users] Coarse Grain using martinize.py

[jagannath mondal]

Dear Tsjerk
  I had a similar question. I guess insane.py script is supposed to build a
coarse-grained membrane/solvent system from scratch. But, if I already have
a particular existing atomistic configuration of lipid/water system along
with some proteins ( which I had obtained by performing an atomistic
simulation), how do I generate a coarse-grained martini counter-part of
that specific atomistic snapshot ?

Your suggestion will be very helpful.

jagannath


On Sat, Feb 27, 2016 at 3:29 AM, Tsjerk Wassenaar  wrote:

> Hi Ali,
>
> The current version of martinize is for coarse graining proteins and
> there's a version for nucleic acids. Lipids are not supported yet. These
> you could forward map with the program backward, but why the hassle as you
> can also directly build the coarse grain membrane/solvent system with
> insane (http://www.cgmartini.nl/index.php/downloads/tools/239-insane).
>
> Hope it helps,
>
> Tsjerk
> On Feb 26, 2016 22:36,  wrote:
>
>
>
> Dear all
> I want to simulate a system of 128 DPPC with 3655 water molecule which its
> .pdb file is available on professor tielman website. I want to Coarse
> grain it but apparently at first i should turn the pdb file into
> appropriate type for using with martini. I understood, I should use marti
> ize.py to convert the pdb but I dont know how. Also the tutorial wasnt
> helpful. Could anyone give me the direct command to do this ?
> best regards
> Ali
> ==
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
> Department of Mechanical Engineering
> Sharif University of Technology, Tehran, Iran
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[gmx-users] generating martini-version of lipids

[Jagannath Mondal]

Dear Gromacs/Martini-users

I wanted to transform a snapshot of my atomistic DPPG/water bilayer to the
Martini coarse-grained format. However, I found martinize.py script  does
not transform lipid or waters to coarse-grained counterpart.It only works
for protein. So, Is there any particular way I can generate the CG version
of my atomistic DPPG/water bilayer ?

I guess backward scripts does the reverse of what I am trying to achieve.
So, if you can suggest a way to generate a coarse-grained pdb files of the
atomistic lipid bilayer/water, that will be very helpful.

Jagannath
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[gmx-users] How to generate intermediates for alchemy mutation

[Jagannath Mondal]

Dear Users
  I want to compute the relative free energy for mutating one residue of a
protein to another one using free energy perturbations as implemented in
gromacs. I wanted to know how I can generate the starting configurations of
the intermediate lambda values. Is there any interpolation scheme within
gromacs that will let me generate the intermediate structures.
Jagannath
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[gmx-users] freeze group in NPT ensemble in gromacs 5.x

[jagannath mondal]

Hi
  Previously, with gromacs 4.5.4, I had not experienced any problem with
freeze group in NPT ensemble . However, in gromacs 5.0, the same simulation
is crashing. Any suggestion regarding what is best setup for freeze group
calculation in NPT ensemble in gromacs 5.x
Jagannath
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Re: [gmx-users] how to maintain planarity of graphene sheet

[jagannath mondal]

Hi Vitaly

  Unfortunately, the paper does not mention anything about whether the
forcefields for graphene were taken from OPLS or AMBER.
If I could get  the topology file  (even for part of) the graphene , it
would have been  very helpful. I could have replicated and improvised the
topology files for the graphene size I am interested in.
Jagannath

On Fri, Jan 15, 2016 at 6:14 AM, VITALY V. CHABAN <vvcha...@gmail.com>
wrote:

> The force constants were either from OPLS or from AMBER (which of these is
> referenced in the paper?)
>
>
>
> On Thu, Jan 14, 2016 at 5:40 PM, jagannath mondal <jm3...@columbia.edu>
> wrote:
>
> > Hi Vitaly
> >   Thanks for pointing to the paper.
> >   Based on the paper, "GR was simulated as a non-polarizable assembly of
> > carbon atoms linked by harmonic potentials with the following bonded
> > parameters: distance (C–C)= 1.41 nm, angle (C–C–C) = 120 , dihedral
> (C–C–C
> > –C) =0 "
> >  Can you please specify what were the values of force-constant used for
> > bonds, angle and dihedrals ?
> > Jagannath
> >
> >
> >
> > On Thu, Jan 14, 2016 at 6:53 PM, VITALY V. CHABAN <vvcha...@gmail.com>
> > wrote:
> >
> >> By using high force constants for all bonded terms.
> >>
> >> An ideally planar graphene in the solution/dispersion is an unphysical
> >> model though. You must read literature for further insights:
> >>
> >>
> >>
> http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra16857k#!divAbstract
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Thu, Jan 14, 2016 at 5:13 AM, jagannath mondal <jm3...@columbia.edu>
> >> wrote:
> >>
> >> > Hi
> >> >
> >> >   Which restraints can one  use to maintain planarity of graphene
> sheets
> >> > while performing MD simulations of their association ? I guess
> >> > flat-bottommed restraints will not work.
> >> >
> >> > Jagannath
> >> > --
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[gmx-users] query on umbrella sampling of association of two plates

[Jagannath Mondal]

Dear Gromacs users

  I wanted to calculate PMF of association of two graphene plates using
umbrella sampling simulations. However, my concern is how we can maintain
the planer configuration of two plates along xy-planes while performing the
umbrella sampling along the separation along z direction. Does one need to
use any special restraint in gromacs ?

Thanks

jagannath
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[gmx-users] How to generate a model beta sheet

[Jagannath Mondal]

Dear all
  Is there a tool or method to generate coordinates of  a model beta sheet
structure for a given  sequence ?

Jagannath
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[gmx-users] forcefield parameter for bromide ion

[jagannath mondal]

Hi
  I need to do a simulation of protein in presence of LiBr salt solution.
However, I am not finding any force field parameters for bromide ion either
in charmm forcefields or amber forcefields. Can someone suggest a decent
source for bromide ion forcefield parameters that one could employ in
simulation involving protein.
Jagannath
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[gmx-users] How to create a spherocylindrical wall

[Jagannath Mondal]

Hi
  I would like to perform a simulation ( without any periodic boundary
condition) where I need to have a wall of spherocylindrical geometry. In
other words the particles will be confined inside a spherocylinder.

 Is there any good suggestion on how to achieve that in gromacs?

1) One option I thought of achieving that is by having a spherocylindrical
wall potential.  Is there a way of putting the wall potential in the form
of a table-potential ? (Not sure cylinder option in gromacs umbrella
sampling  not going to be helpful).

2)  Or,should I put a bunch of hard sphere which constitute the
spherocylindrical boundary so that the particles inside the spherocylinder
will have a repulsive interaction each time they come towards the boundary ?

Thanks
Jagannath
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[gmx-users] problem with gpu performance

[jagannath mondal]

Dear Gromacs Users

  I am trying to run gpu version of gromacs5.0.6 in a work-station which is
a hexacore processor that can be multithreaded to 12. The workstation has 2
Geforce GT  610 GPUs . I am finding the simulation using -nb gpu is
exceedingly slower than -nb cpu ( i,e turning off gpu)

I installed cuda-7.0 and using this I could install gpu version of gromacs
5.0.6 as follows.

cmake ../ -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_INSTALL_PREFIX=/home/jmondal/UTIL/GROMACS_5.0.6_gpu/
-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++  -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/


However,  the performance with gpu is very weird. If I do mdrun using
following command:
1) gmx mdrun -s topol. -nb gpu -v &>log_run

and then repeat the same thing by turning of gpu usage

2) gmx mdrun -s topol -nb cpu -v >& log_run

using gpus, the performance drops about 3 times !! Using both the GPUs
along with CPUs, the performance is: 1.620 ns/day
  using only CPUs, the performance is 4.6 ns/day... usage of GPUs is
frustratingly slowing down the performance.

when using -nb gpu option, gromacs md.log correctly detects gpu and cpu as
follows:

Using 2 MPI threads
Using 6 OpenMP threads per tMPI thread

Detecting CPU SIMD instructions.
Present hardware specification:
Vendor: GenuineIntel
Brand:  Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
Family:  6  Model: 63  Stepping:  2
Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx
msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2
sse3 sse4.1 sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX2_256


2 GPUs detected:
  #0: NVIDIA GeForce GT 610, compute cap.: 2.1, ECC:  no, stat: compatible
  #1: NVIDIA GeForce GT 610, compute cap.: 2.1, ECC:  no, stat: compatible

2 GPUs auto-selected for this run.
Mapping of GPUs to the 2 PP ranks in this node: #0, #1


However, when I look at the performance at the end of the simulation, the
'wait GPU nonlocal' takes awfully long time.
I also tried few other options ( such as using only 1 gpu using gpu_id 0 ).
Also played with ntmpi and ntomp option. But GPUs performance is
drastically poor ( surprisingly 3 times slower than only cpu-based
simulation),

I am struggling to figure out whether it is a hardware issue or GPU-driver
issue or whether I am not using best optimal option.
Your suggestion will be useful in solving the issue.
Jagannath


   R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 2 MPI ranks, each using 6 OpenMP threads

 Computing:  Num   Num  CallWall time Giga-Cycles
 Ranks Threads  Count  (s) total sum%
-
 Domain decomp. 26 63   0.270 11.322   0.2
 DD comm. load  26 13   0.000  0.002   0.0
 Neighbor search26 63   0.311 13.062   0.2
 Launch GPU ops.26   5002   0.205  8.614   0.2
 Comm. coord.   26   2438   0.239 10.016   0.2
 Force  26   2501   1.358 57.011   1.0
 Wait + Comm. F 26   2501   0.404 16.954   0.3
 PME mesh   26   2501   9.734408.587   7.3
 Wait GPU nonlocal  26   2501 117.798   4944.651  88.3
 Wait GPU local 26   2501   0.005  0.206   0.0
 NB X/F buffer ops. 26   9878   0.255 10.683   0.2
 Write traj.26  4   0.180  7.558   0.1
 Update 26   2501   0.807 33.886   0.6
 Constraints26   2501   1.216 51.025   0.9
 Comm. energies 26126   0.001  0.055   0.0
 Rest   0.609 25.573   0.5
-
 Total133.392   5599.205 100.0
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Re: [gmx-users] problem with gpu performance

[jagannath mondal]

Hi Peter
  Thanks for your response. I also realized that GTX-610 is not able to
catch up with the faster cpu ( Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz). I
tried cpu-gpu combination for -nb option. It improves it slightly but not
by much. So, we are planning to go for a replacement of GPU cards.
At this point, we have two plans: either go for single 4 GB GTX-970 or two
2 GB GTX-960 . I was wondering whether you can comment on which options
will be better as far as performance is concerned.
Thanks for your input
jagannath

On Fri, Sep 4, 2015 at 6:45 PM, Peter Kroon <p.c.kr...@rug.nl> wrote:

> Hi Jagannath,
>
> AFAIK GT610's are rather slow. What you could try is using both cpu and
> gpu for non-bonded interactions (-nb gpu_cpu)
>
> Peter
>
> On 04/09/15 15:01, jagannath mondal wrote:
> > Dear Gromacs Users
> >
> >   I am trying to run gpu version of gromacs5.0.6 in a work-station which
> is
> > a hexacore processor that can be multithreaded to 12. The workstation
> has 2
> > Geforce GT  610 GPUs . I am finding the simulation using -nb gpu is
> > exceedingly slower than -nb cpu ( i,e turning off gpu)
> >
> > I installed cuda-7.0 and using this I could install gpu version of
> gromacs
> > 5.0.6 as follows.
> >
> > cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> > -DCMAKE_INSTALL_PREFIX=/home/jmondal/UTIL/GROMACS_5.0.6_gpu/
> > -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++  -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/
> >
> >
> > However,  the performance with gpu is very weird. If I do mdrun using
> > following command:
> > 1) gmx mdrun -s topol. -nb gpu -v &>log_run
> >
> > and then repeat the same thing by turning of gpu usage
> >
> > 2) gmx mdrun -s topol -nb cpu -v >& log_run
> >
> > using gpus, the performance drops about 3 times !! Using both the GPUs
> > along with CPUs, the performance is: 1.620 ns/day
> >   using only CPUs, the performance is 4.6 ns/day... usage of GPUs is
> > frustratingly slowing down the performance.
> >
> > when using -nb gpu option, gromacs md.log correctly detects gpu and cpu
> as
> > follows:
> >
> > Using 2 MPI threads
> > Using 6 OpenMP threads per tMPI thread
> >
> > Detecting CPU SIMD instructions.
> > Present hardware specification:
> > Vendor: GenuineIntel
> > Brand:  Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
> > Family:  6  Model: 63  Stepping:  2
> > Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx
> > msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2
> > sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > SIMD instructions most likely to fit this hardware: AVX2_256
> > SIMD instructions selected at GROMACS compile time: AVX2_256
> >
> >
> > 2 GPUs detected:
> >   #0: NVIDIA GeForce GT 610, compute cap.: 2.1, ECC:  no, stat:
> compatible
> >   #1: NVIDIA GeForce GT 610, compute cap.: 2.1, ECC:  no, stat:
> compatible
> >
> > 2 GPUs auto-selected for this run.
> > Mapping of GPUs to the 2 PP ranks in this node: #0, #1
> >
> >
> > However, when I look at the performance at the end of the simulation, the
> > 'wait GPU nonlocal' takes awfully long time.
> > I also tried few other options ( such as using only 1 gpu using gpu_id 0
> ).
> > Also played with ntmpi and ntomp option. But GPUs performance is
> > drastically poor ( surprisingly 3 times slower than only cpu-based
> > simulation),
> >
> > I am struggling to figure out whether it is a hardware issue or
> GPU-driver
> > issue or whether I am not using best optimal option.
> > Your suggestion will be useful in solving the issue.
> > Jagannath
> >
> >
> >R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
> >
> > On 2 MPI ranks, each using 6 OpenMP threads
> >
> >  Computing:  Num   Num  CallWall time Giga-Cycles
> >  Ranks Threads  Count  (s) total sum%
> >
> -
> >  Domain decomp. 26 63   0.270 11.322
>  0.2
> >  DD comm. load  26 13   0.000  0.002
>  0.0
> >  Neighbor search26 63   0.311 13.062
>  0.2
> >  Launch GPU ops.26   5002   0.205  8.614
>  0.2
> >  Comm. coord.   26   2438   0.239 10.016
>  0.2
> >  Force  26   2501   1.358 57.011
>  1.0
> >  Wait + Comm. F