[gmx-users] Question about COM-Pulling

[Christian Mücksch]

Dear Chris,

thx a lot for your help!

Unfortunately, the information you provided is nowhere to be found in the 
manual.

With best wishes,
Christian


--
for your setup options, the spring potential is something like:

U=0.5*k*[(z_ref - z_pull) - (initial_dist + time*0.01)]^2

(please refer to the manual for more details, I don't do AFM and didn't check 
the exact functional form).

So the spring is not on the displacement but on the difference between the 
actual displacement and the desired displacement, where your desired 
displacement is changing over time.

Chris.

-- original message --



/  > Here you have time, the z position of your reference group and the

/>/  > difference along z between your pull group and your reference group.
/>/  > There is no "dummy particle" as the spring extends between the
/>/  > "reference" group at z=1.1675 and the "pull" group, which in the 
first
/>/  > frame is located at z=1.1675 + 3.47701.
/>/  >
/>/  > I have used the pull code since v3.3.1 and I do not recall there ever
/>/  > being a dummy particle when using:
/>/  >
/>/  > pull = umbrella
/>/  > pull_geometry = distance
/>/  >
/>/  > It is the distance of the restraint that changes over time in your 
setup.
/Sorry to ask again but I'm a bit confused. I thought that a spring (harmonic 
potential)
is connected to the pull-group (by "dummy-particle" I meant the top of the 
spring=zspring)
and then moved at a certain pull_rate in the desired direction.

If the spring extends from the pull-group to the reference group and the 
reference group stays in place while the pull-group is moved away,
then the spring would extend and extend and therefore the force rise and rise. 
What obvious fact am I missing?

Is there a difference between AFM pulling and Umbrella pulling?

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[gmx-users] Question about COM-Pulling

[Christian Mücksch]

 Here you have time, the z position of your reference group and the
 difference along z between your pull group and your reference group.
 There is no "dummy particle" as the spring extends between the
 "reference" group at z=1.1675 and the "pull" group, which in the first
 frame is located at z=1.1675 + 3.47701.

 I have used the pull code since v3.3.1 and I do not recall there ever
 being a dummy particle when using:

 pull = umbrella
 pull_geometry = distance

 It is the distance of the restraint that changes over time in your setup.


Sorry to ask again but I'm a bit confused. I thought that a spring (harmonic 
potential)
is connected to the pull-group (by "dummy-particle" I meant the top of the 
spring=zspring)
and then moved at a certain pull_rate in the desired direction.

If the spring extends from the pull-group to the reference group and the 
reference group stays in place while the pull-group is moved away,
then the spring would extend and extend and therefore the force rise and rise. 
What obvious fact am I missing?

Is there a difference between AFM pulling and Umbrella pulling?


On 10-12-13 01:29 PM,gmx-users-request at gromacs.org  
  wrote:

/  ubject: [gmx-users] Question about COM-Pulling

/>/  To: MAILINGLIST GROMACShttp://lists.gromacs.org/mailman/listinfo/gmx-users>>
/>/  Message-ID:<4D065C09.4020809 at rhrk.uni-kl.de  
>
/>/  Content-Type: text/plain; charset=UTF-8; format=flowed
/>/
/>/  Hi,
/>/
/>/  although this is not relevant to my previous question:
/
It is indeed relevant.


/  I used mdrun like this:

/>/
/>/  mdrun -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr
/>/  -g pull.log -px pull_dist.xvg -pf pull_force.xvg
/>/
/>/  With an input-file like this:
/>/
/>/  
/>/  ; Run-Parameter
/>/  integrator = md
/>/  dt = 0.002
/>/  nsteps = 100
/>/
/>/  ; OUTPUT CONTROL OPTIONS
/>/  nstxout = 5000
/>/  nstvout = 5000
/>/  nstfout = 5000
/>/  nstlog = 5000
/>/  nstenergy = 5000
/>/
/>/  pull_nstxout = 100 ;
/>/  pull_nstfout = 100 ;
/>/
/>/  rlist = 1.2
/>/  ns_type = grid
/>/  coulombtype = PME-Switch
/>/  rcoulomb = 1.0
/>/  vdw-type = shift
/>/  rvdw = 1.0
/>/  rvdw_switch = 0.9
/>/  pbc = xyz
/>/
/>/  tcoupl = V-rescale
/>/  tc-grps = Protein Non-Protein
/>/  tau_t = 0.1 0.1
/>/  ref_t = 300 300
/>/
/>/  pcoupl = Berendsen
/>/  pcoupltype = isotropic
/>/  tau_p = 2
/>/  ref_p = 1
/>/  compressibility = 4.5e-5
/>/
/>/  DispCorr = EnerPres
/>/  continuation = yes
/>/
/>/  constraint_algorithm = lincs
/>/  constraints = all-bonds
/>/
/>/  pull = umbrella
/>/  pull_geometry = distance
/>/  pull_dim = N N Y
/>/  pull_start = yes
/>/  pull_ngroups = 1
/>/  pull_group0 = reference
/>/  pull_group1 = pull
/>/  pull_rate1 = 0.01
/>/  pull_k1 = 1000
/>/  
/>/
/>/  ...I get an output for pull_dist.xvg which looks sth. like this:
/>/
/>/  
/>/  # This file was created Fri Nov 26 16:22:53 2010
/>/  # by the following command:
/>/  # /mnt/nas1/c_muecksch/GROMACS_4.5.3/bin/mdrun_mpi_4.5.3_s -v -s
/>/  pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log
/>/  -px pull_dist.xvg -pf pull_force.xvg
/>/  #
/>/  # mdrun_mpi_4.5.3_s is part of G R O M A C S:
/>/  #
/>/  # Grunge ROck MAChoS
/>/  #
/>/  @ title "Pull COM"
/>/  @ xaxis label "Time (ps)"
/>/  @ yaxis label "Position (nm)"
/>/  @TYPE xy
/>/  @ view 0.15, 0.15, 0.75, 0.85
/>/  @ legend on
/>/  @ legend box on
/>/  @ legend loctype view
/>/  @ legend 0.78, 0.8
/>/  @ legend length 2
/>/  @ s0 legend "0 Z"
/>/  @ s1 legend "1 dZ"
/>/  0. 1.1675 3.47701
/>/  0.2000 1.1675 3.48043
/>/  0.4000 1.1675 3.4795
/>/  0.6000 1.1675 3.48214
/>/  0.8000 1.1675 3.4869
/>/
/>/  and so on
/
Here you have time, the z position of your reference group and the
difference along z between your pull group and your reference group.
There is no "dummy particle" as the spring extends between the
"reference" group at z=1.1675 and the "pull" group, which in the first
frame is located at z=1.1675 + 3.47701.

I have used the pull code since v3.3.1 and I do not recall there ever
being a dummy particle when using:

pull = umbrella
pull_geometry = distance

It is the distance of the restraint that changes over time in your setup.

Chris.




/  

/>/
/>/  In this pull_dist.xvg there is no position of a "dummy"-particle that is
/>/  connected via a harmonic potential to the pull group (as described in
/>/  GrubmuÌ^ller, Helmut ; Heymann, Berthold ; Tavan, Paul: Ligand Binding:
/>/  Molecular Mechanics Calculation of the StreptavidinâEUR"Biotin Rupture
/>/  Force. In: Science 271 (1996))
/>/
/>/  In older version of Gromacs I believe that this was the case. Has the
/>/  method changed? How is the force calculated if not by the displacmen

[gmx-users] Question about COM-Pulling

[Christian Mücksch]

Hi,

although this is not relevant to my previous question:

I used mdrun like this:

mdrun -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr 
-g pull.log -px pull_dist.xvg -pf pull_force.xvg


With an input-file like this:


; Run-Parameter
integrator = md
dt = 0.002
nsteps = 100

; OUTPUT CONTROL OPTIONS
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstenergy = 5000

pull_nstxout = 100 ;
pull_nstfout = 100 ;

rlist = 1.2
ns_type = grid
coulombtype = PME-Switch
rcoulomb = 1.0
vdw-type = shift
rvdw = 1.0
rvdw_switch = 0.9
pbc = xyz

tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300

pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 2
ref_p = 1
compressibility = 4.5e-5

DispCorr = EnerPres
continuation = yes

constraint_algorithm = lincs
constraints = all-bonds

pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = reference
pull_group1 = pull
pull_rate1 = 0.01
pull_k1 = 1000


...I get an output for pull_dist.xvg which looks sth. like this:


# This file was created Fri Nov 26 16:22:53 2010
# by the following command:
# /mnt/nas1/c_muecksch/GROMACS_4.5.3/bin/mdrun_mpi_4.5.3_s -v -s 
pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log 
-px pull_dist.xvg -pf pull_force.xvg

#
# mdrun_mpi_4.5.3_s is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@ title "Pull COM"
@ xaxis label "Time (ps)"
@ yaxis label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0. 1.1675 3.47701
0.2000 1.1675 3.48043
0.4000 1.1675 3.4795
0.6000 1.1675 3.48214
0.8000 1.1675 3.4869

and so on


In this pull_dist.xvg there is no position of a "dummy"-particle that is 
connected via a harmonic potential to the pull group (as described in 
Grubmüller, Helmut ; Heymann, Berthold ; Tavan, Paul: Ligand Binding: 
Molecular Mechanics Calculation of the Streptavidin–Biotin Rupture 
Force. In: Science 271 (1996))


In older version of Gromacs I believe that this was the case. Has the 
method changed? How is the force calculated if not by the displacment of the
"dummy"-particle. I just wanted to know how the afm pulling in gromacs 
is achieved without having to look in the source-code.


Thx,
Christian


---
Dear Christian:

As per my original comments, please provide a .mdp file, sample
output, and all the other things that I asked for.

Chris.

--original message--

this is a more general question.

I thought that in analogy to an AFM-experiment a "dummy"-particle is placed
at a certain distance from the center of mass of the pull group (compare
figure 6.1 in the manual).
The force is then calculated as the displacement between the pulled atom
and the
"dummy"-particle. So if this is true which I'm not sure of,
I was wondering why the position of this "dummy"-particle is not plotted.

Or does this umbrella pulling work in a different way? How is the force
calculated?

Thanks a lot,
Christian

--
The position of the reference group and the displacement of the pulled
group from the reference group should be printed (although perhaps
without the reference position if you are using absolute coordinate
pulling, which is not recommended anyhow).

If you want some better advice, please be more specific and include
cut and paste sections saying "I expected X at Y, but it was not in
the file Z.xvg". you should also include your pull-code .mdp options
and your grompp and mdrun commands.

Chris.

-- original message --

Dear users,

I've got a short question regarding com-pulling. From what I understand
Umbrella pulling is the same as AFM pulling using a harmonic potential.

Why is the position of the spring in the pullx.xvg not printed? One can
only find the vector between both pull groups. I looked into older
Gromacs manuals and in versions < 4 it seems as if this data is printed
to the pullx.xvg file or something similar.

With kind regards,
Christian


--
Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Email: mueck...@rhrk.uni-kl.de

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[gmx-users] Question about COM-Pulling

[Christian Mücksch]

Hi,

this is a more general question.

I thought that in analogy to an AFM-experiment a "dummy"-particle is placed
at a certain distance from the center of mass of the pull group (compare 
figure 6.1 in the manual).
The force is then calculated as the displacement between the pulled atom 
and the

"dummy"-particle. So if this is true which I'm not sure of,
I was wondering why the position of this "dummy"-particle is not plotted.

Or does this umbrella pulling work in a different way? How is the force 
calculated?


Thanks a lot,
Christian

--
The position of the reference group and the displacement of the pulled
group from the reference group should be printed (although perhaps
without the reference position if you are using absolute coordinate
pulling, which is not recommended anyhow).

If you want some better advice, please be more specific and include
cut and paste sections saying "I expected X at Y, but it was not in
the file Z.xvg". you should also include your pull-code .mdp options
and your grompp and mdrun commands.

Chris.

-- original message --

Dear users,

I've got a short question regarding com-pulling. From what I understand
Umbrella pulling is the same as AFM pulling using a harmonic potential.

Why is the position of the spring in the pullx.xvg not printed? One can
only find the vector between both pull groups. I looked into older
Gromacs manuals and in versions < 4 it seems as if this data is printed
to the pullx.xvg file or something similar.

With kind regards,
Christian

--
Christian Mücksch

--
Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Fax:   +49 (0)631 205 4965
Email: mueck...@rhrk.uni-kl.de

--
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[gmx-users] Question about COM-Pulling

[Christian Mücksch]

Dear users,

I've got a short question regarding com-pulling. From what I understand 
Umbrella pulling is the same as AFM pulling using a harmonic potential.


Why is the position of the spring in the pullx.xvg not printed? One can 
only find the vector between both pull groups. I looked into older 
Gromacs manuals and in versions < 4 it seems as if this data is printed 
to the pullx.xvg file or something similar.


With kind regards,
Christian

--
Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Fax:   +49 (0)631 205 4965
Email: mueck...@rhrk.uni-kl.de

--
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[gmx-users] Problem with coulombtype=user and 1,4 interactions

[Christian Mücksch]

Dear Gromacs experts,

I've been trying to use a tabulated potential for the 
coulombic-interactions with all Gromacs versions from 4.0.7 to 4.5.3.


In combination with OPLS/AA force field and SPC/E water I used a 
potential by Gezelter for a simple system consisting of a protein in 
Water+Ions:
Fennell, Christopher J. ; Gezelter, J. D.: Is the Ewald summation still 
necessary? Pairwise alternatives to the accepted standard for long–range 
elec- trostatics. In: Journal of Chemical Physics 124 (2006)


When I run mdrun I specify sth. like this:
mdrun_mpi_s -table table_gezelter_s.xvg -tablep table_gezelter_s.xvg -v 
-deffnm file.tpr


My problem is that the 14 Coulomb-energy is approximately half the value 
of that compared to PME-switch.
The Coulomb-SR energy is approximately at the same value as PME and 
everything else works alright.


So there's sth. wrong with the 1,4 energies. Since OPLS/AA uses a 
scaling factor of 1/2 for the 1,4-interactions changing it will mess up 
the whole simulation since the 1,4 LJ energies will get wrong. If I use 
another table for the 1,4 interactions multiplied by a factor of 2 
everything gets worse.


As a consequence this potential fails to reproduce densities etc.

So what am I missing? Is it the potential that's wrong?

Thanks alot for any ideas!
Christian

--
Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Fax:   +49 (0)631 205 4965
Email: mueck...@rhrk.uni-kl.de


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[gmx-users] Role of epsilon_rf in implicit solvation

[Christian Mücksch]

Dear users,

I've got yet another question about the implicit solvent models used in 
Gromacs. I saw in some simulations that epsilon_rf was set to 0 meaning 
infinite dielectric constant. The manual is not clear about this, since 
it is mentioned in combination with reaction field only.


So is this epsilon_rf also used in combination in implicit solvent 
models regarding the dielectric constant beyond cut-off? If yes, what 
would be an appropriate value for this constant?


Best regards,
Christian

--
Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Fax:   +49 (0)631 205 4965
Email: mueck...@rhrk.uni-kl.de

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[gmx-users] Re: GB-polarization

[Christian Mücksch]

But in order to get the complete solvation free energy these 
calculations for the van der Waals and cavity terms have to be done.
So does that mean that the solvation free energy calculated by default 
without specifying "sa_algorithm=Ace-approximation" is missing these terms?


I thought that the ACE-type approximation is done by default (due to the 
manual) when using GBSA.


Kind regards,
Christian


Christian Mücksch wrote:


>  Thanks for the clarification but I can't find anything in the .log or
>  .edr-files that would correspond to the non-polar solvation energy.
>  

I think you have to set "sa_algorithm=Ace-approximation" for this calculation to
be done, and thus written.

-Justin



>  Christian Mücksch
>  Department of Physics
>  TU Kaiserslautern
>  Erwin Schrödinger Straße
>  67663 Kaiserslautern
>  Germany
>  
>  Phone: +49 (0)631 205 4287

>  Fax:   +49 (0)631 205 4965
>  Email:mueck...@rhrk.uni-kl.de
>  
>  
>  

>>  Hi! Yes, the GB-polarization energy corresponds to the solvent-solute
>>  electrostatics polarization energy. The non-polar part of the
>>  solvation energy (the solvent-solvent cavity term and the
>>  solute-solvent vdw-term) are named Non. polar solvation (or something
>>  like that) in the log-file. /Per 4 nov 2010 kl. 11.10 skrev Christian
>>  Mücksch:

>>>  >Dear all,
>>>  >>   I've got a general question regarding implicit solvent

>>>  simulations.

>>>  >Using g_energy there's an option to print out the GB-polarization.

>>>  Is that the solvent-solute electrostatics polarization free energy?

>>>  >>   How can one interpret a rise or decrease in the GB-polarization?
>>>  >>   Kind regards,
--  Justin A. Lemkul Ph.D. 
Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of 
Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 
231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 




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[gmx-users] Re: GB-polarization

[Christian Mücksch]

Thanks for the clarification but I can't find anything in the .log or 
.edr-files that would correspond to the non-polar solvation energy.


Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Fax:   +49 (0)631 205 4965
Email: mueck...@rhrk.uni-kl.de



Hi! Yes, the GB-polarization energy corresponds to the solvent-solute 
electrostatics polarization energy. The non-polar part of the 
solvation energy (the solvent-solvent cavity term and the 
solute-solvent vdw-term) are named Non. polar solvation (or something 
like that) in the log-file. /Per 4 nov 2010 kl. 11.10 skrev Christian 
Mücksch:

>  Dear all,
>  
>  I've got a general question regarding implicit solvent simulations.

>  Using g_energy there's an option to print out the GB-polarization. Is that 
the solvent-solute electrostatics polarization free energy?
>  
>  How can one interpret a rise or decrease in the GB-polarization?
>  
>  Kind regards,

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[gmx-users] GB-polarization

[Christian Mücksch]

Dear all,

I've got a general question regarding implicit solvent simulations.
Using g_energy there's an option to print out the GB-polarization. Is 
that the solvent-solute electrostatics polarization free energy?


How can one interpret a rise or decrease in the GB-polarization?

Kind regards,

--
Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Email: mueck...@rhrk.uni-kl.de

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[gmx-users] about sa_surface_tension

[Christian Mücksch]

 Dear all,

when using implicit solvent models, the sa_surface_tension parameter is 
set to 2.092 kJ/mol/nm2 by default.


However in Gromacs benchmarks with dihydrofolate reductase this 
parameter is set to 2.25936.


Can someone please explain this parameter and in how far this would 
change the simulation outcome.


Kind regards,

--
Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Email: mueck...@rhrk.uni-kl.de

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[gmx-users] About implicit water simulations

[Christian Mücksch]

 Dear users,

I got a question concerning simulations with implicit solvent. So far it 
is only possible to use this model when applying a cut-off for the long 
range electrostatic and vdW interactions which leads to bad energy 
conservation etc.


Will there be an update allowing to use reaction-field for instance or 
user-defined potentials with implicit solvent models?


Best regards,
Christian Mücksch

--
Christian Mücksch  Phone: +49 (0)631 205 4287
Department of Physics  Fax:   +49 (0)631 205 4965
TU Kaiserslautern  Email: mueck...@rhrk.uni-kl.de
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

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[gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5

[Christian Mücksch]

 Dear all,

so I downloaded Gromacs-4.5 and tried to compile the gpu-version with 
cmake version 2.8.0 as stated in the gpu installation instructions as


export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5
make mdrun
make install-mdrun

But I get a few errors:

-
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- CTest cannot determine repository type. Please set UPDATE_TYPE to 
'cvs' or 'svn'. CTest update will not work.

CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message):
  CPack license resource file:
  "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallLicense.txt"
  could not be found.
Call Stack (most recent call first):
  /usr/share/cmake-2.8/Modules/CPack.cmake:707 (cpack_check_file_exists)
  CMakeLists.txt:40 (include)


CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message):
  CPack readme resource file:
  "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallInfo.txt"
  could not be found.
Call Stack (most recent call first):
  /usr/share/cmake-2.8/Modules/CPack.cmake:708 (cpack_check_file_exists)
  CMakeLists.txt:40 (include)


CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message):
  CPack welcome resource file:
  "/home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallWelcome.txt"
  could not be found.
Call Stack (most recent call first):
  /usr/share/cmake-2.8/Modules/CPack.cmake:709 (cpack_check_file_exists)
  CMakeLists.txt:40 (include)


-- Performing Test CFLAGS_WARN
-- Performing Test CFLAGS_WARN - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Failed
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN
-- Performing Test CXXFLAGS_WARN - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Failed
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- No external FFT libraries needed for the OpenMM build, using fftpack!
-- Threads not compatible with OpenMM build, disabled!
CMake Warning at CMakeLists.txt:183 (message):
  CPU-based acceleration turned off, OpenMM does not support/need any!


-- Looking for include files HAVE_STRING_H
-- Looking for include files HAVE_STRING_H - found
-- Looking for include files HAVE_MATH_H
-- Looking for include files HAVE_MATH_H - found
-- Looking for include files HAVE_LIMITS_H
-- Looking for include files HAVE_LIMITS_H - found
-- Looking for include files HAVE_MEMORY_H
-- Looking for include files HAVE_MEMORY_H - found
-- Looking for include files HAVE_UNISTD_H
-- Looking for include files HAVE_UNISTD_H - found
-- Looking for include files HAVE_PWD_H
-- Looking for include files HAVE_PWD_H - found
-- Looking for include files HAVE_STDINT_H
-- Looking for include files HAVE_STDINT_H - found
-- Looking for include files HAVE_STDLIB_H
-- Looking for include files HAVE_STDLIB_H - found
-- Looking for include files HAVE_PTHREAD_H
-- Looking for include files HAVE_PTHREAD_H - found
-- Looking for include files HAVE_DIRENT_H
-- Looking for include files HAVE_DIRENT_H - found
-- Looking for include files HAVE_INTTYPES_H
-- Looking for include files HAVE_INTTYPES_H - found
-- Looking for include files HAVE_REGEX_H
-- Looking for include files HAVE_REGEX_H - found
-- Looking for include files HAVE_SYS_TYPES_H
-- Looking for include files HAVE_SYS_TYPES_H - found
-- Looking for include files HAVE_SYS_STAT_H
-- Looking for include files HAVE_SYS_STAT_H - found
-- Looking for include files HAVE_SYS_TIME_H
-- Looking for include files HAVE_SYS_TIME_H - found
-- Looking for include files HAVE_RPC_RPC_H
-- Looking for include files HAVE_RPC_RPC_H - found
-- Looking for include files HAVE_RPC_XDR_H
-- Looking for include files HAVE_RPC_XDR_H - found
-- Looking for include files HAVE_XMMINTRIN_H
-- Looking for include files HAVE_XMMINTRIN_H - found
-- Looking for include files HAVE_EMMINTRIN_H
-- Looking for include files HAVE_EMMINTRIN_H - found
-- Looking for include files HAVE_PMMINTRIN_H
-- Looking for include files HAVE_PMMINTRIN_H - not found.
-- Looking for include files HAVE_SMMINTRIN_H
-- Looking for include files HAVE_SMMINTRIN_H - not found.
-- Looking for include files HAVE_IO_H
-- Looking for include files HAVE_IO_H - not found.
-- Looking for strcasecmp
-- 

[gmx-users] Problems with GPU-Version and implicit water models

[Christian Mücksch]

 Dear all,

I am using Gromacs-4.5-beta4 and compiled the GPU-Version. So far only 
Amber-FF are working in the GPU-version. When I want to use the GBSA 
implicit water-model I have to use cut-off for the electrostatic 
interactions due to this error-message:


ERROR 1 [file PR.mdp]:
  With GBSA, coulombtype must be equal to Cut-off

Now, my problem is that the GPU-version does not accept cut-off for the 
electrostatic interactions since only options like Reaction-Field,  
Ewald,  PME and No-cutoff are supported so I get the following error:


---
Program mdrun-gpu_beta, VERSION 4.5-beta4
Source code file: ../gromacs-4.5-beta4/src/kernel/openmm_wrapper.cpp, 
line: 1038


Fatal error:
Internal error: you should not see this message, it means that 
theelectrosatics option check failed. Please report this error!

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Will there be an update allowing to use implicit-water with 
reaction-field on the GPU? Will it be possible to use other ff like 
OPLSAA on the GPU?


Kind regards,
Christian Muecksch
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[gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny

[Christian Mücksch]

Dear All,

I've been trying to compile and get Gromacs (version 4.0.7) working on a 
cluster that runs with Debian Lenny.


I set the following variables:
export SOFT=$HOME/GROMACS
export PATH="$PATH":$SOFT/bin
export LDFLAGS="-L$SOFT/lib"
export CPPFLAGS="-I$SOFT/include"
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SOFT/lib
export MPICC=$SOFT/bin/mpicc

and then did

./configure --prefix=$SOFT --disable-float --program-suffix=_mpi_d 
--enable-mpi


after I installed the Gromacs-version without mpi. Before configuring 
Gromacs I compiled the latest version of OPEN-MPI with gcc-4.3.
I did exactly the same on another cluster that runs with Debian Etch and 
everything worked fine and was pretty straightforward.


Here I get the following error during configuring:

checking whether your compiler can handle assembly files (*.s)... no
configure: error: Upgrade your compiler (or disable assembly loops)

The exact error from the config.log looks like this:

configure:32822: checking whether your compiler can handle assembly 
files (*.s)
configure:32841: /usr/bin/mpicc  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -c conftestasm.s

conftestasm.s: Assembler messages:
conftestasm.s:2: Error: bad register name `%rsp'
configure:32844: $? = 1
configure:32857: result: no
configure:32859: error: Upgrade your compiler (or disable assembly loops).

When I compiled Gromacs with the --disable-x86-64-sse option, then my 
submitted jobs run extremely slow compared to the other cluster.
Although MPI is running and the CPU-loads are all 100% the speed is 
nearly as slow as running on a single CPU.
I also tried compiling with MVAPICH with is already installed on the 
cluster but I get the same error.


Unfortunately I could not compile OPEN-MPI with the follwing flags:
export CC="gcc-4.3 -m64"
export CXX="g++-4.3 -m64"
export F77="gfortran-4.3 -m64"

Do you have any idea what could be the cause of the problem so that I 
can tell the Cluster-Admin what specific package to install?
Any help would be deeply appreciated since I'm new to this whole MPI 
topic and I could not find a way around this problem.


Thanks a lot,
Christian

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