Re: [gmx-users] auto-correlation time

[Netaly Khazanov]

Thank you Mark for your replay.

I've followed the potential energy term.
This is exactly what I did.

Regards,
Netaly

On Wed, Jan 10, 2018 at 1:04 AM, Mark Abraham 
wrote:

> Hi,
>
> You can calculate the autocorrelation time of an observable, but not of a
> whole simulation. Tools like gmx energy and gmx analyse have such
> functionality, if you identify an observable of interest.
>
> Mark
>
> On Sun, Jan 7, 2018 at 2:33 PM Netaly Khazanov  wrote:
>
> > Hi All,
> > I've performed REMD simulation and now I am wondering how to calculate
> > auto-correlation time of the simulation in order to be sure that it is
> > large than replica exchange frequency.
> > Any help will be appreciated.
> > Netaly
> >
> >
> > --
> > Netaly
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[gmx-users] Worse GROMACS performance with better specs?

[Jason Loo Siau Ee]

Dear gmx users,



I recently purchased a second GPU workstation and tried compiling GROMACS on 
it, but despite the better (and more expensive) specs the performance is 
significantly worse on my test system. To test things I standardized the 
version (2016.4). Some details below:



Workstation 1:

2 x Intel Xeon E5-2680v4 (14 cores), 2 x GTX 1080

gmx mdrun -ntmpi 8 -ntomp 7 -gpu_id 

Performance: 61ns/day



Workstation 2:

2 x Intel Xeon Gold 6126 (12 cores), 2 x GTX 1080Ti

gmx mdrun -ntmpi 8 -ntomp 6 -gpu_id 

Performance: 49ns/day



I'm guessing it's an issue during compilation but I can't figure it out. I 
wouldn't claim to have any knowledge about how GROMACS interacts with the 
hardware, so some observations as below (not sure idea which is actually 
relevant):



- Compilation command for both: cmake .. -DGMX_BUILD_OWN_FFTW=ON  
-DREGRESSIONTEST_DOWNLOAD=ON  -DGMX_GPU=ON  -DCMAKE_INSTALL_PREFIX=/opt/gromacs



- When compiling on Workstation 2 I originally got a CMake error "Cannot find 
AVX512F compiler flag". Updated my gcc version to 5.3.1 to solve this.



- Some regression tests fail for Workstation 2 during compilation: 4 
-FTUnitTest (SEGFAULT), 16 - CorrelationTest



- mdrun logs show Hardware Topology: Basic versus Hardware Topology: Only 
logical processor count



- Running CPU-only (export CUDA_VISIBLE_DEVICES="") I get 21ns/day versus 23 
ns/day , so the CPUs in Workstation 2 are definitely faster.



- Upgraded both to 2018.rc1 (used cmake3) I get a regression test fail for 
Workstation 1 (9 - GPUUtilUnitTest) and Workstation 2 (8 - FFTUnitTests, 9 - 
GPUUtilsUnitTest, 26 - CorrelationTest). Performance is 66.5ns/day versus 
51.95ns/day. The GPU load actually looks similar to previous versions (~70% for 
Workstation 1 and 50-60% for Workstation 2). I actually got the best 
performance with Workstation 1 running 2016.1 (69ns/day).



Any help on how I can optimize performance on Workstation 2 would be 
appreciated. If there are certain files that would be helpful let me know and 
I'll send a link.



Cheers,
Jason







Jason Loo

PhD, MPharm, RPh

Lecturer

School of Pharmacy

Faculty of Health and Medical Sciences

Taylor's University



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Re: [gmx-users] resuming run

[Rose]

No it's first part of my job

Sent from my iPhone

> On Jan 10, 2018, at 2:37, Mark Abraham  wrote:
> 
> Hi,
> 
> Extending simulations is covered at
> http://manual.gromacs.org/documentation/2016.4/user-guide/managing-simulations.html
> but
> whether you can hope to reproduce a published finding depends on quite a
> few things.
> 
> Mark
> 
>> On Tue, Jan 9, 2018 at 6:31 PM rose rahmani  wrote:
>> 
>> Hi;
>> 
>> i'm doing umbrella sampling. When i compare the PMF with literature it's
>> similar in TREND, but peaks are not as sharp as literature( my system and
>> literature are very similar ). if i increase the simulation time(for
>> example from 4ns to 40ns), is there any possibility that i maybe see the
>> sharp peaks in my sytem too?if yes, how can i run simulation to continue
>> the run just after 4ns (to 40ns) NOT again from 0ns?
>> 
>> With regards
>> --
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Re: [gmx-users] lambda value for free energy calculation

[kordzadeh]

Hi Dr.Abraham 

Thank you very much for your answer 

excuse me but, I didnt understand

I want to calculate free energy of drug in water and I want to consider 
VDW,coulombic and bonding interation with these lambda value

vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00  1.00 1.00 1.00 ... 
1.00 

 coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 1.00 1.00 1.00  ... 
1.00 
 
 bonded_lambdas=0.00 0.00 0.00 ... 0.00 0.00 0.00 0.00 ... 0.00 0.00 0.05  0.10 
... 1.00

I think I dont need mass , temperature and restraint value , however I 
dont know application of them exactly

probably when temperature and mass change ,we use those lambda value and when 
we have a restraint in system we use restraint  lambda value.

excuse me for elementary question

Im beginner with Gromacs

Thank you very  much for your help

Regards

Azadeh

 

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Re: [gmx-users] MBAR bootstrap

[Michael Shirts]

This is not the right place to ask about MBAR.  You could pose the question
on https://github.com/choderalab/pymbar if you have specific questions
about how to implement something there.
https://github.com/MobleyLab/alchemical-analysis is a wrapper for MBAR that
can process gromacs files.

See:
http://www.alchemistry.org/wiki/Analyzing_Simulation_Results#Bootstrap_Sampling
for a discussion of bootstrap sampling in the context of free energies.

On Tue, Jan 9, 2018 at 8:01 PM, Thanh Le  wrote:

> Hi everyone,
> I have a question regarding using bootstrap for MBAR.
> After running 30 windows for the complex and 20 windows for the ligand,
> 100 ns each, I have a problem trying to do bootstrap (based on what I have
> read, bootstrap sampling is recommended to analyze results from MBAR)
> Can anyone point me to the correct direction to implement bootstrap? Or
> any advice on how to analyze MBAR?
> Thanks,
> Thanh Le
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[gmx-users] MBAR bootstrap

[Thanh Le]

Hi everyone, 
I have a question regarding using bootstrap for MBAR.
After running 30 windows for the complex and 20 windows for the ligand, 100 ns 
each, I have a problem trying to do bootstrap (based on what I have read, 
bootstrap sampling is recommended to analyze results from MBAR)
Can anyone point me to the correct direction to implement bootstrap? Or any 
advice on how to analyze MBAR?
Thanks,
Thanh Le
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Re: [gmx-users] resuming run

[Mark Abraham]

Hi,

Extending simulations is covered at
http://manual.gromacs.org/documentation/2016.4/user-guide/managing-simulations.html
but
whether you can hope to reproduce a published finding depends on quite a
few things.

Mark

On Tue, Jan 9, 2018 at 6:31 PM rose rahmani  wrote:

> Hi;
>
> i'm doing umbrella sampling. When i compare the PMF with literature it's
> similar in TREND, but peaks are not as sharp as literature( my system and
> literature are very similar ). if i increase the simulation time(for
> example from 4ns to 40ns), is there any possibility that i maybe see the
> sharp peaks in my sytem too?if yes, how can i run simulation to continue
> the run just after 4ns (to 40ns) NOT again from 0ns?
>
> With regards
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] GROMACS-GPU enabled installation error

[Mark Abraham]

Hi,

On Sat, Jan 6, 2018 at 10:21 PM Joydeep Munshi  wrote:

> Hello,
>
> I am trying to install Gromacs 5.1.5 with GPU enabled version. I have
> Nvidia Geforce GTX1080 GPU card in my system and Cuda 9.1.85 installed as
>

That version of the code is much older than the CUDA or GPU you are using.
Recent versions of CUDA don't support things that the versions that were
around in 5.1.5 did, so your best strategy is to use a more recent GROMACS
version that is aware of the new CUDA behaviour.

Mark


> my nvcc. While running cmake command as mentioned below, I am succssfully
> able to generate the makefiles in build directory. However, while running
> make after that, I am facing with an error. Could you please help me out
> with resolving the issue?
>
> *cmake *comamnd used before running *make*:
>
> *cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=on-DGMX_BUILD_MDRUN_ONLY=on
> -DGMX_BINARY_SUFFIX=_cuda  -DGMX_LIBS_SUFFIX=_cuda
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.1*
>
>
> *make *error:
>
>  */bin/mkdir -p
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/lib/pkgconfig'*
> * /usr/bin/install -c -m 644 fftw3f.pc
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/lib/pkgconfig'*
> *Making install in threads*
> *Making install in tests*
> *Making install in mpi*
> *Making install in doc*
> *Making install in FAQ*
> * /bin/mkdir -p
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'*
> * /usr/bin/install -c -m 644
>
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/
> fftw3.info
> 
>
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-1
>
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-2
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'*
> * install-info
>
> --info-dir='/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info/
> fftw3.info
> '*
> *Making install in tools*
> * /bin/mkdir -p
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
> *  /bin/bash ../libtool   --mode=install /usr/bin/install -c fftwf-wisdom
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
> *libtool: install: /usr/bin/install -c fftwf-wisdom
>
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin/fftwf-wisdom*
> * /bin/mkdir -p
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
> * /usr/bin/install -c fftw-wisdom-to-conf
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
> * /bin/mkdir -p
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/man/man1'*
> * /usr/bin/install -c -m 644
>
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/tools/fftw-wisdom-to-conf.1
> fftwf-wisdom.1
>
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/man/man1'*
> *Making install in m4*
> *[  0%] Completed 'fftwBuild'*
> *[  0%] Built target fftwBuild*
> *[  0%] Generating baseversion-gen.c*
> *[  1%] Building NVCC (Device) object
>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o*
> *nvcc fatal   : Unsupported gpu architecture 'compute_20'*
> *CMake Error at libgromacs_generated_copyrite_gpu.cu.o.cmake:207
> (message):*
> *  Error generating*
> *
>
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o*
>
>
> *src/gromacs/CMakeFiles/libgromacs.dir/build.make:63: recipe for target
>
> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o'
> failed*
> *make[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o]
> Error 1*
> *CMakeFiles/Makefile2:1291: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed*
> *make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2*
> *Makefile:160: recipe for target 'all' failed*
> *make: *** [all] Error 2*
>
> *Thanks and regards,*
> *Joydeep Munshi,*
> *Graduate Research Assistant,*
> *Packard Lab 375,*
> *Mechanical Engineering and Mechanics,*
> *Lehigh University*
> *Contact: (484)-821-6702*
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> 

Re: [gmx-users] auto-correlation time

[Mark Abraham]

Hi,

You can calculate the autocorrelation time of an observable, but not of a
whole simulation. Tools like gmx energy and gmx analyse have such
functionality, if you identify an observable of interest.

Mark

On Sun, Jan 7, 2018 at 2:33 PM Netaly Khazanov  wrote:

> Hi All,
> I've performed REMD simulation and now I am wondering how to calculate
> auto-correlation time of the simulation in order to be sure that it is
> large than replica exchange frequency.
> Any help will be appreciated.
> Netaly
>
>
> --
> Netaly
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Re: [gmx-users] Force field informations

[Mark Abraham]

Hi,

There's lots of discussion in the reference manual, and also in the force
field files themselves.

Mark

On Mon, Jan 8, 2018 at 4:28 PM Lara rajam  wrote:

> Dear GMX users
> I would like to know where we would get the force field information in GMX
> .
> Like in NAMD the Topology and parm file tells the details of the atom
> labeling,charge,connectivity etc., Simillarly where I could see the Gromos
> force field insights.
> Please provide me links or tutorials that will be very useful
> Thank you
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Re: [gmx-users] GPU ECC question

[Mark Abraham]

Hi,

On Mon, Jan 8, 2018 at 6:05 PM Kevin Chen  wrote:

>
> Dear GMX users
>
> We are in the process of evaluating GPU/CPU options for an in-house cluster
> to carry out MD simulations using GromacsV2016. We appreciate if anyone
> could provide us answers for the following questions regarding the impact
> on
> ECC on Gromacs GPU calculations. Generally we want to know (and have
> references for)
>

See some discussion in https://arxiv.org/abs/1507.00898. There are also
several published works considering the impact of ECC on AMBER, whose
results are broadly applicable to GROMACS, too.


> 1) How often these errors occur?
>

Very seldom. Obviously the rate will vary from device to device.


> 2) Can Gromacs along with ECC detect and correct for these errors?


I've no idea. There's no code in GROMACS that manages anything actively.

3) How robust are the algorithms governing MD against these types of errors?
>

See those publications. The overwhlemingly likely result is an enormous
force on a single particle, which would immediately lead to the simulation
crashing.


> 4) Is the time and resource overhead from ECC even worth it?
>

No.

Mark


> Thanks in advance!
>
> Kevin Chen
>
>
>
>
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Re: [gmx-users] lambda value for free energy calculation

[Mark Abraham]

Hi,

Did you understand why the tutorial recommended turning on VDW before
coulomb? Does that reasoning apply to other interactions?

Mark

On Tue, Jan 9, 2018 at 5:33 AM  wrote:

> Hi all
>
> I have aquestion about free energy calculation
>
> as  in tutorial be said if we want to consider coloumbic interaction we
> must define lambda as follows:
>
> vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00
>
> coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00
>
> if I want to consider bonded interaction should I write:
>
> vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00  1.00 1.00 1.00
> ... 1.00
>
> coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 1.00 1.00 1.00
> ... 1.00
>
> bonded_lambdas=0.00 0.00 0.00 ... 0.00 0.00 0.00 0.00 ... 0.00 0.00 0.05
> 0.10 ... 1.00
>
> when should we consider temperature_lambdas,
> mass_lambdas,restraint_lambdas?
>
> Thank you very much for your help
>
> Regards
>
> Azadeh
>
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Re: [gmx-users] Minimization problem

[Mark Abraham]

Hi,

You're also using tabulated VDW interactions, so I'd start by looking at
that. What steps have you taken to ensure that each of your topologies
works, e.g. on their own in vacuum?

Mark

On Tue, Jan 9, 2018 at 11:46 PM Neda Rafiee  wrote:

> Dear Users,
> I have a problem in energy minimization step. Actually I have some groups
> of atoms that are freezed and also a chain of protein in water. I want the
> following items:
> constraints =  none
> integrator  =  steep
> emstep  =  0.0001
> emtol   =  500.0
> nsteps  =  50
> ; Neighbor list and pbc's --
> cutoff-scheme   =  group
> nstlist =  1; default is 10 -- try more frequent
> ns_type =  grid ; simple (for no pbc) or grid
> ;
> pbc =  xyz  ; CHANGE
> periodic_molecules  =  no
> ;
> ; Interaction parameters ---
> rlist   =  1
> rlistlong   =  1
> rcoulomb=  1
> ;
> coulombtype =  PME
> epsilon_r   =  1
> ;
> vdwtype =  user; cut-off
> rvdw=  1
>
> but after just 6000 steps it gives me this error:
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 500 (which may not be possible for your system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 53429 steps,
> but did not reach the requested Fmax < 500.
> Potential Energy  =  2.46705107676305e+14
> Maximum force =  9.69602643026733e+08 on atom 9415
> Norm of force =  1.70746371816015e+07
>
> Would you please help me understand where the problem is ?!
> Thanks
> Neda
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[gmx-users] Minimization problem

[Neda Rafiee]

Dear Users,
I have a problem in energy minimization step. Actually I have some groups of 
atoms that are freezed and also a chain of protein in water. I want the 
following items:
constraints =  none
integrator  =  steep
emstep  =  0.0001
emtol   =  500.0
nsteps  =  50
; Neighbor list and pbc's --
cutoff-scheme   =  group
nstlist =  1; default is 10 -- try more frequent
ns_type =  grid ; simple (for no pbc) or grid
;
pbc =  xyz  ; CHANGE
periodic_molecules  =  no
;
; Interaction parameters ---
rlist   =  1
rlistlong   =  1
rcoulomb=  1
;
coulombtype =  PME
epsilon_r   =  1
;
vdwtype =  user; cut-off
rvdw=  1 

but after just 6000 steps it gives me this error:
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 500 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 53429 steps,
but did not reach the requested Fmax < 500.
Potential Energy  =  2.46705107676305e+14
Maximum force =  9.69602643026733e+08 on atom 9415
Norm of force =  1.70746371816015e+07

Would you please help me understand where the problem is ?!
Thanks
Neda
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[gmx-users] resuming run

[rose rahmani]

Hi;

i'm doing umbrella sampling. When i compare the PMF with literature it's
similar in TREND, but peaks are not as sharp as literature( my system and
literature are very similar ). if i increase the simulation time(for
example from 4ns to 40ns), is there any possibility that i maybe see the
sharp peaks in my sytem too?if yes, how can i run simulation to continue
the run just after 4ns (to 40ns) NOT again from 0ns?

With regards
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[gmx-users] Time step in umbrella sampling

[rose rahmani]

Hi;

i'm doing umbrella sampling.i did pulling of AA from surface  and then
different conformation with trjconv and then umbrella sampling.i
thought that 0.9 nm was the closest distance from surface because when i
changed the pullratejust for 0.001 nm/ns the run crashed, so ithought it
couldn't be closer more.so i run md for umbrella then gmx wham.
but when i check and draw the profile.xvg file, energy had  min value in
0.6 nm! and was repulsive in closer distances. i didn't sample any closer
distance from 0.9 nm and didn't md_umbrella run for it because i didn't see
closer distances in summary distances.datfile(token fro gmx distance).How
could be possible?i didn't know it before.
Then i modified the dt to half of its former value and increased nsteps
2times so there is not any change in simulation time,BUT at this time i got
the closer distances(in comparison with 0.9 nm), 0.5 nm!
HOW can i be sure that dt=X is the best value and my AA will not be closer
more even i change the simulation time or pullrate or anything else?
Before these happenings i thought that when the run doesn't crush
everything is OK, but now i don't have any idea!
could you please help me?

Thank you so much
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[gmx-users] Vacuum in the hydrophobic part of bilayers

[Mohsen Ramezanpour]

Hi Gromacs users,

In the hydrophobic part of the bilayers, there are some spaces (especially
in the mid-layer) which is not completely filled with atoms (so, vacuum).

I was wondering if there is any tool which is capable of measuring this
(i.e. the volume of this space) in bilayers?

Thanks in advance for your reply,
Mohsen
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Re: [gmx-users] energy minimization

[rose rahmani]

On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul  wrote:

>
>
> On 1/6/18 10:10 AM, rose rahmani wrote:
>
>> Hi,
>>
>> I want to calculate the number of density profile of water.the initial
>> .gro
>> file which i have,has amino acid in itself, which should not be present in
>> this analyze. So, i had to remove amino acid, and then, when i wanted to
>> do
>> energy minimization again, it's crushed and gave me step files.
>> maybe it's because of modifying the initial gro file but i didn't have any
>> choice i think so! because i have another structures in initial.gro file
>> which i don't want to modify their coordinates.and all structure are in
>> the
>> center of box and the rest of the box should be empty.
>> would you please help me? what is the alternative?
>>
>
> Why do you have to remove the amino acid to do this analysis?

I should study different amino acids one by one in my system.In literature
there is just  one NUMBER density profile scheme reported for all
different( in amino acids) tests. This means that this profile should  not
depend on amino acids and should be token before amino acid is in. it's
rational because as you said amino acid can change the distribution of
water also its number density so different amino acids cause different
changes, am i wrong?
However in literature a few distance above surface is considered (1nm) and
my amino acids are in about 1.7 far from surface ( because i want to do
pulling in next step)but i think it's better to remove it( as i have not
access to file before amino acid is in so i thought maybe it's better to
remove it and do EM and equilibration again). What do you think,sir?
BTW, how can i specify the gmx density to just calculate the specific
distance above surface not whole box (Z dimension) ?

Thank you

>

You're creating a rather large void, which will make nearby waters
> unstable. In the analysis, you're going to have a volume occupied by the
> amino acid that yields zero water density. That's going to happen
> irrespective of whether or not you remove the amino acid, so save yourself
> some trouble and don't mess with the coordinates.
>
> -Justin
>
>
> with regards
>>
>>
>>
>>
>> this is em.job
>>
>> Steepest Descents:
>> Tolerance (Fmax)   =  1.0e+01
>> Number of steps= 5000
>> Step=0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom=
>> 815
>> Step=1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom=
>> 4307
>> Step=2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom=
>> 4307
>> Step=3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom=
>> 4302
>> Step=4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom=
>> 4303
>> Step=5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom=
>> 4303
>> Step=6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom=
>> 4303
>> Step=7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom=
>> 4303
>> Step=8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom=
>> 4303
>> Step=9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom=
>> 4303
>> Step=   10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom=
>> 4302
>> Step=   11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom=
>> 4302
>> Step=   12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom=
>> 4301
>> Step=   13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom=
>> 4303
>>
>> step 14: Water molecule starting at atom 2018 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>>
>> step 14: Water molecule starting at atom 1265 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>> Wrote pdb files with previous and current coordinates
>> Wrote pdb files with previous and current coordinates
>> Step=   14, Dmax= 1.1e-01 nm, Epot=  2.77257e+05 Fmax= 2.29207e+09, atom=
>> 2018^M
>> step 15: Water molecule starting at atom 1331 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>> Wrote pdb files with previous and current coordinates
>> Step=   15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom=
>> 1331^MStep=   16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02,
>> atom= 4301
>> Step=   17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom=
>> 4303
>> Step=   18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom=
>> 4301
>> Step=   19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom=
>> 4301
>> Step=   20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom=
>> 4301
>> Step=   21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom=
>> 4301
>>
>> 140,1
>> .
>> .
>> .
>> .
>>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of 

Re: [gmx-users] dimensions of the box

[RAHUL SURESH]

Thank you all

On Tue, 9 Jan 2018 at 6:33 PM, Justin Lemkul  wrote:

>
>
> On 1/8/18 6:18 AM, RAHUL SURESH wrote:
> > Dear all
> >
> > For a protein-ligand simulation,
> >
> > for the command
> >
> > gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 1.0 -c
> >
> > Read 680 atoms
> > Volume: 25.6402 nm^3, corresponds to roughly 11500 electrons
> > No velocities found
> >  system size :  3.411 17.359  3.004 (nm)
> >  diameter: 17.543   (nm)
> >  center  :  5.138 15.619  2.935 (nm)
> >  box vectors :  3.411  2.687  2.798 (nm)
> >  box angles  :  90.00  90.00  90.00 (degrees)
> >  box volume  :  25.64   (nm^3)
> >  shift   :  4.633 -5.847  6.837 (nm)
> > new center  :  9.771  9.771  9.771 (nm)
> > new box vectors : 19.543 19.543 19.543 (nm)
> > new box angles  :  90.00  90.00  90.00 (degrees)
> > new box volume  :7463.88   (nm^3)
> >
> > System size looks so large, which eventually consume more computational
> > time. For 100ps nvt/npt it takes around 6 hours, which normally gets done
> > in 3-5 mins..
>
> Sounds like you're comparing apples and oranges and hoping for the same
> result; just because system X runs at a given speed doesn't mean system
> Y will. You have a system here that is extended along the y-axis,
> requiring a huge box. That's inherently going to run pretty slow, since
> the box is cubic and about an order of magnitude larger in each
> dimension than an "average" system.
>
> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] fep protocol for gromacs 2016

[Mark Abraham]

Hi,

You need to have VDW on any atom that has a charge, or opposite charges are
at risk of collison. I think your lambda schedule is the wrong way around.

Mark

On Tue, Jan 9, 2018 at 4:23 PM  wrote:

> Dear Yoav,
>
> Hi, did you use a soft-core technique?
> In which lambda range do you have large free energy differences?
>
> Best,
> Asaf
>
> Quoting Yoav Atsmon-Raz :
>
> > Hi everyone,
> >
> > I’ve been trying to get a the free energy difference between a
> > leucine residue vs an alanine residue by doing a set of FEP
> > simulations in which I decouple the VDW and electrostatic
> > interactions in the martini CG force field. In the particular
> > example I’m using here, I’m aiming to decouple the Leucine sidechain
> > and the topology I’m using is as follows:
> > --
> > [ moleculetype ]
> > ; Name Exclusions
> > Protein_A 1
> >
> > [ atoms ]
> > 1P5 1   TRPBB 1  0. P5   0  72
> > 2   SC4 1   TRP   SC1 2  0. SC4  0  72
> > 3   SNd 1   TRP   SC2 3  0. SNd  0  72
> > 4   SC5 1   TRP   SC3 4  0. SC5  0  72
> > 5   SC5 1   TRP   SC4 5  0. SC5  0  72
> > 6   Nda 2   LEUBB 6  0. Nda  0  72
> > 7   AC1 2   LEU   SC1 7  0. AC1  0  72
> > 8   Nda 3   LEUBB 8  0. Nda  0  72
> > 9   AC1 3   LEU   SC1 9  0. DUM  0  72
> >10   Nda 4   LEUBB10  0. Nda  0  72
> >11   AC1 4   LEU   SC111  0. AC1  0  72
> >12Qa 5   LEUBB12 -1. Qa  -1  72
> >13   AC1 5   LEU   SC113  0. AC1  0  72
> >
> > [ bonds ]
> > ; Backbone bonds
> > 1 6  1   0.35000  1250 ; TRP(E)-LEU(E)
> > 6 8  1   0.35000  1250 ; LEU(E)-LEU(E)
> > 810  1   0.35000  1250 ; LEU(E)-LEU(E)
> >1012  1   0.35000  1250 ; LEU(E)-LEU(E)
> > ; Sidechain bonds
> > 1 2  1   0.3  5000 ; TRP
> > 6 7  1   0.33000  7500 ; LEU
> > 8 9  1   0.33000  7500 ; LEU
> >1011  1   0.33000  7500 ; LEU
> >1213  1   0.33000  7500 ; LEU
> > ; Short elastic bonds for extended regions
> > 1 8  1   0.64000  2500 ; TRP(1)-LEU(8) 1-3
> > 610  1   0.64000  2500 ; LEU(6)-LEU(10) 2-4
> > 812  1   0.64000  2500 ; LEU(8)-LEU(12) 2-4
> > ; Long elastic bonds for extended regions
> > 110  1   0.97000  2500 ; TRP(1)-LEU(10) 1-4
> > 612  1   0.97000  2500 ; LEU(6)-LEU(12) 1-4
> >
> > [ constraints ]
> > 2 3  1   0.27000 ; TRP
> > 2 4  1   0.27000 ; TRP
> > 3 4  1   0.27000 ; TRP
> > 3 5  1   0.27000 ; TRP
> > 4 5  1   0.27000 ; TRP
> > [ angles ]
> > ; Backbone angles
> > 1 6 8  213425 ; TRP(E)-LEU(E)-LEU(E)
> > 6 810  213425 ; LEU(E)-LEU(E)-LEU(E)
> > 81012  213425 ; LEU(E)-LEU(E)-LEU(E)
> > ; Backbone-sidechain angles
> > 2 1 6  210025 ; TRP(E)-LEU(E) SBB
> > 1 6 7  210025 ; TRP(E)-LEU(E) SBB
> > 6 8 9  210025 ; LEU(E)-LEU(E) SBB
> > 81011  210025 ; LEU(E)-LEU(E) SBB
> >101213  210025 ; LEU(E)-LEU(E) SBB
> > ; Sidechain angles
> > 1 2 3  221050 ; TRP
> > 1 2 4  2 9050 ; TRP
> >
> > [ dihedrals ]
> > ; Backbone dihedrals
> > ; Sidechain improper dihedrals
> > 1 3 4 2  2  050 ; TRP
> > 2 3 5 4  2  0   200 ; TRP
> > ---
> >
> >
> > The mdp I’m using goes like this:
> >
> > -
> > ; Run control
> > integrator   = sd   ; Langevin dynamics
> > tinit= 0
> > dt   = 0.02
> > nsteps   = 5000   ; 1 us
> > nstcomm  = 100
> > comm-grps= Protein_A Water
> > ; Output control
> > nstxout  = 0
> > nstvout  = 0
> > nstfout  = 0
> > nstlog   = 1000
> > nstenergy= 100
> > nstxout-compressed   = 1000
> > compressed-x-precision   = 10
> > compressed-x-grps= Protein_A Water
> > energygrps   = Protein_A Water
> > ; Neighborsearching and short-range nonbonded interactions
> > cutoff-scheme= verlet
> > verlet-buffer-tolerance  = 0.005
> > nstlist  = 20
> > ns_type  = grid
> > pbc  = xyz
> > ; Electrostatics
> > coulombtype  = reaction-field
> > rcoulomb = 1.1
> > epsilon_r= 15
> > epsilon_rf   = 0
> > ; van der Waals
> > vdwtype  = cutoff
> > vdw-modifier 

Re: [gmx-users] fep protocol for gromacs 2016

[asaffarhi]

Dear Yoav,

Hi, did you use a soft-core technique?
In which lambda range do you have large free energy differences?

Best,
Asaf

Quoting Yoav Atsmon-Raz :


Hi everyone,

I’ve been trying to get a the free energy difference between a  
leucine residue vs an alanine residue by doing a set of FEP  
simulations in which I decouple the VDW and electrostatic  
interactions in the martini CG force field. In the particular  
example I’m using here, I’m aiming to decouple the Leucine sidechain  
and the topology I’m using is as follows:

--
[ moleculetype ]
; Name Exclusions
Protein_A 1

[ atoms ]
1P5 1   TRPBB 1  0. P5   0  72
2   SC4 1   TRP   SC1 2  0. SC4  0  72
3   SNd 1   TRP   SC2 3  0. SNd  0  72
4   SC5 1   TRP   SC3 4  0. SC5  0  72
5   SC5 1   TRP   SC4 5  0. SC5  0  72
6   Nda 2   LEUBB 6  0. Nda  0  72
7   AC1 2   LEU   SC1 7  0. AC1  0  72
8   Nda 3   LEUBB 8  0. Nda  0  72
9   AC1 3   LEU   SC1 9  0. DUM  0  72
   10   Nda 4   LEUBB10  0. Nda  0  72
   11   AC1 4   LEU   SC111  0. AC1  0  72
   12Qa 5   LEUBB12 -1. Qa  -1  72
   13   AC1 5   LEU   SC113  0. AC1  0  72

[ bonds ]
; Backbone bonds
1 6  1   0.35000  1250 ; TRP(E)-LEU(E)
6 8  1   0.35000  1250 ; LEU(E)-LEU(E)
810  1   0.35000  1250 ; LEU(E)-LEU(E)
   1012  1   0.35000  1250 ; LEU(E)-LEU(E)
; Sidechain bonds
1 2  1   0.3  5000 ; TRP
6 7  1   0.33000  7500 ; LEU
8 9  1   0.33000  7500 ; LEU
   1011  1   0.33000  7500 ; LEU
   1213  1   0.33000  7500 ; LEU
; Short elastic bonds for extended regions
1 8  1   0.64000  2500 ; TRP(1)-LEU(8) 1-3
610  1   0.64000  2500 ; LEU(6)-LEU(10) 2-4
812  1   0.64000  2500 ; LEU(8)-LEU(12) 2-4
; Long elastic bonds for extended regions
110  1   0.97000  2500 ; TRP(1)-LEU(10) 1-4
612  1   0.97000  2500 ; LEU(6)-LEU(12) 1-4

[ constraints ]
2 3  1   0.27000 ; TRP
2 4  1   0.27000 ; TRP
3 4  1   0.27000 ; TRP
3 5  1   0.27000 ; TRP
4 5  1   0.27000 ; TRP
[ angles ]
; Backbone angles
1 6 8  213425 ; TRP(E)-LEU(E)-LEU(E)
6 810  213425 ; LEU(E)-LEU(E)-LEU(E)
81012  213425 ; LEU(E)-LEU(E)-LEU(E)
; Backbone-sidechain angles
2 1 6  210025 ; TRP(E)-LEU(E) SBB
1 6 7  210025 ; TRP(E)-LEU(E) SBB
6 8 9  210025 ; LEU(E)-LEU(E) SBB
81011  210025 ; LEU(E)-LEU(E) SBB
   101213  210025 ; LEU(E)-LEU(E) SBB
; Sidechain angles
1 2 3  221050 ; TRP
1 2 4  2 9050 ; TRP

[ dihedrals ]
; Backbone dihedrals
; Sidechain improper dihedrals
1 3 4 2  2  050 ; TRP
2 3 5 4  2  0   200 ; TRP
---


The mdp I’m using goes like this:

-
; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.02
nsteps   = 5000   ; 1 us
nstcomm  = 100
comm-grps= Protein_A Water
; Output control
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 1000
nstenergy= 100
nstxout-compressed   = 1000
compressed-x-precision   = 10
compressed-x-grps= Protein_A Water
energygrps   = Protein_A Water
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
verlet-buffer-tolerance  = 0.005
nstlist  = 20
ns_type  = grid
pbc  = xyz
; Electrostatics
coulombtype  = reaction-field
rcoulomb = 1.1
epsilon_r= 15
epsilon_rf   = 0
; van der Waals
vdwtype  = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = Protein_A Water
tau_t= 1.0 1.0
ref_t= 300 300
; Pressure coupling is on for NPT
Pcoupl   = Berendsen
Pcoupltype   = isotropic
tau_p=  5.0
compressibility  = 3e-04 3e-04
ref_p= 1.0 1.0
; Free energy control stuff
free_energy  = yes
init_lambda_state= 0
delta_lambda = 0
calc_lambda_neighbors= -1; only immediate neighboring windows
; Vectors 

Re: [gmx-users] lambda value for free energy calculation

[dgfd dgdfg]

>when should we consider temperature_lambdas, mass_lambdas,restraint_lambdas?
If hamiltonian of the system changes between initial and final states the 
corresponding part is given in
coul-lambdas
vdw-lambdas
bonded-lambdas
restraint-lambdas
mass-lambdas

temperature-lambdas change the external conditions (state of the thermostat) 
and used only for simulated tempering ( 
http://manual.gromacs.org/documentation/2018-rc1/user-guide/mdp-options.html#free-energy-calculations
 ) 
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Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/7/18 3:07 AM, negar habibzadeh wrote:

I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
your tutorial  When I use inflategro script For my System I have got
Output System_inflated.gro file with certain message in Command prompt
as follows  . The Below Message Shows That There is No Lipid Molecules
Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
Molecules Need to be Deleted ?


Maybe there just aren't any lipids overlapping with the protein; that 
can happen.


-Justin


There are 128 lipids...
with 138 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 0 lipids within cut-off range...
0 will be removed from the upper leaflet...
0 will be removed from the lower leaflet...

Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 2441
Protein Y-min/max: 2343
X-range: 17 AY-range: 20 A
Building 17 X 20 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD
lower TMD
Area per protein: 3.25 nm^2
Area per lipid: 10.7582741393 nm^2

Area per protein, upper half: 2.25 nm^2
Area per lipid, upper leaflet : 10.7738991393 nm^2

Area per protein, lower half: 2.5 nm^2
Area per lipid, lower leaflet : 10.7699928893 nm^2

Writing Area per lipid...
Done!


--
==

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.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] energy minimization

[Justin Lemkul]

On 1/6/18 10:10 AM, rose rahmani wrote:

Hi,

I want to calculate the number of density profile of water.the initial .gro
file which i have,has amino acid in itself, which should not be present in
this analyze. So, i had to remove amino acid, and then, when i wanted to do
energy minimization again, it's crushed and gave me step files.
maybe it's because of modifying the initial gro file but i didn't have any
choice i think so! because i have another structures in initial.gro file
which i don't want to modify their coordinates.and all structure are in the
center of box and the rest of the box should be empty.
would you please help me? what is the alternative?


Why do you have to remove the amino acid to do this analysis? You're 
creating a rather large void, which will make nearby waters unstable. In 
the analysis, you're going to have a volume occupied by the amino acid 
that yields zero water density. That's going to happen irrespective of 
whether or not you remove the amino acid, so save yourself some trouble 
and don't mess with the coordinates.


-Justin


with regards




this is em.job

Steepest Descents:
Tolerance (Fmax)   =  1.0e+01
Number of steps= 5000
Step=0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom=
815
Step=1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom=
4307
Step=2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom=
4307
Step=3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom=
4302
Step=4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom=
4303
Step=5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom=
4303
Step=6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom=
4303
Step=7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom=
4303
Step=8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom=
4303
Step=9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom=
4303
Step=   10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom=
4302
Step=   11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom=
4302
Step=   12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom=
4301
Step=   13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom=
4303

step 14: Water molecule starting at atom 2018 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 14: Water molecule starting at atom 1265 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=   14, Dmax= 1.1e-01 nm, Epot=  2.77257e+05 Fmax= 2.29207e+09, atom=
2018^M
step 15: Water molecule starting at atom 1331 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom=
1331^MStep=   16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02,
atom= 4301
Step=   17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom=
4303
Step=   18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom=
4301
Step=   19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom=
4301
Step=   20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom=
4301
Step=   21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom=
4301

140,1
.
.
.
.


--
==

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.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Error while installing GROMACS-2018-rc1

[Mark Abraham]

Hi,

Please do try again when we make the formal release shortly. If there's
still an issue, we'd really appreciate hearing from you, e.g. open a
redmine issue and attach a full output of cmake + make check. But so far,
we think the issue is caused by something outside of anything we can
attempt handle.

Mark

On Tue, Jan 9, 2018 at 10:44 AM Mark Abraham 
wrote:

> Hi,
>
> Thanks again for the testing and feedback.
>
> On Wed, Jan 3, 2018 at 11:52 AM Yongchul Chung 
> wrote:
>
>> Well, celebrated too soon. I received the following error message during
>> "make check" step.
>>
>>
>>
>> NOTE: The GPU has >25% less load than the CPU. This imbalance causes
>>
>>   performance loss.
>>
>>
>>Core t (s)   Wall t (s)(%)
>>
>>Time:0.0340.034  100.0
>>
>>  (ns/day)(hour/ns)
>>
>> Performance:   53.5840.448
>>
>
> Clearly this test ran on a GPU...
>
>
>> Opened
>>
>> /Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr
>> as single precision energy file
>>
>> Reading energy frame 20 time0.020 Reading file
>>
>> /Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr,
>> VERSION 2018-rc1-dev-20180103-871f2f460-unknown (single precision)
>>
>> Can not increase nstlist because an NVE ensemble is used
>>
>> Using 1 MPI thread
>>
>> 1 GPU auto-selected for this run.
>>
>> Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
>>
>>   PP:0
>>
>> Compilation of source file
>> /Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl/
>> nbnxn_ocl_kernels.cl failed!
>>
>> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
>> -DGMX_OCL_FASTGEN_ADD_TWINCUT -DEL_EWALD_ANA -DEELNAME=_ElecEw
>> -DVDWNAME=_VdwLJ -DCENTRAL=22 -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8
>> -DNBNXN_GPU_CLUSTER_SIZE=8 -DNBNXN_GPU_JGROUP_SIZE=4
>> -DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=4 -DNBNXN_MIN_RSQ=3.82e-07f
>> -DIATYPE_SHMEM -cl-fast-relaxed-math
>> -I/Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl
>>
> >
>
>> --LOG START---
>>
>> :80:10: fatal error: 'nbnxn_ocl_kernel_pruneonly.clh' file
>> not found
>>
>> #include "nbnxn_ocl_kernel_pruneonly.clh"
>>
>>  ^
>>
>
> Yet somehow this file was not found shortly afterwards. It's clearly being
> told to look in the right place (from the -I flag in the build options).
> That looks to me like an issue in the OpenCL driver / runtime. I see you're
> using the latest Mac version, but perhaps trying to update the OpenCL
> things will help with a more stable setup.
>
> Mark
>
> ---LOG END
>>
>>
>> ---
>>
>> Program: mdrun-test, version 2018-rc1-dev-20180103-871f2f460-unknown
>>
>> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 502)
>>
>> Function:cl_program gmx::ocl::compileProgram(FILE *, const std::string
>> &, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
>>
>>
>> Internal error (bug):
>>
>> Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 560 Compute Engine
>>
>>   Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE
>>
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>>
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> ---
>>
>>
>>   Start 33: MdrunMpiTests
>>
>> 33/39 Test #33: MdrunMpiTests    Passed2.69 sec
>>
>>   Start 34: regressiontests/simple
>>
>> 34/39 Test #34: regressiontests/simple ...   Passed2.33 sec
>>
>>   Start 35: regressiontests/complex
>>
>> 35/39 Test #35: regressiontests/complex ..   Passed   53.42 sec
>>
>>   Start 36: regressiontests/kernel
>>
>> 36/39 Test #36: regressiontests/kernel ...   Passed   32.33 sec
>>
>>   Start 37: regressiontests/freeenergy
>>
>> 37/39 Test #37: regressiontests/freeenergy ...   Passed5.70 sec
>>
>>   Start 38: regressiontests/pdb2gmx
>>
>> 38/39 Test #38: regressiontests/pdb2gmx ..   Passed   15.66 sec
>>
>>   Start 39: regressiontests/rotation
>>
>> 39/39 Test #39: regressiontests/rotation .   Passed3.10 sec
>>
>>
>> 97% tests passed, 1 tests failed out of 39
>>
>>
>> Label Time Summary:
>>
>> GTest  =  19.86 sec*proc (33 tests)
>>
>> IntegrationTest=  18.38 sec*proc (3 tests)
>>
>> MpiTest=   2.73 sec*proc (3 tests)
>>
>> UnitTest   =   1.48 sec*proc (30 tests)
>>
>>
>> Total Test time (real) = 132.48 sec
>>
>>
>> The following tests FAILED:
>>
>> 32 - MdrunTests (Failed)
>>
>> Errors while running CTest
>>
>> make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
>>
>> make[2]: *** 

Re: [gmx-users] Error while installing GROMACS-2018-rc1

[Mark Abraham]

Hi,

Thanks again for the testing and feedback.

On Wed, Jan 3, 2018 at 11:52 AM Yongchul Chung 
wrote:

> Well, celebrated too soon. I received the following error message during
> "make check" step.
>
>
>
> NOTE: The GPU has >25% less load than the CPU. This imbalance causes
>
>   performance loss.
>
>
>Core t (s)   Wall t (s)(%)
>
>Time:0.0340.034  100.0
>
>  (ns/day)(hour/ns)
>
> Performance:   53.5840.448
>

Clearly this test ran on a GPU...


> Opened
>
> /Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr
> as single precision energy file
>
> Reading energy frame 20 time0.020 Reading file
>
> /Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr,
> VERSION 2018-rc1-dev-20180103-871f2f460-unknown (single precision)
>
> Can not increase nstlist because an NVE ensemble is used
>
> Using 1 MPI thread
>
> 1 GPU auto-selected for this run.
>
> Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
>
>   PP:0
>
> Compilation of source file
> /Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl/
> nbnxn_ocl_kernels.cl failed!
>
> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
> -DGMX_OCL_FASTGEN_ADD_TWINCUT -DEL_EWALD_ANA -DEELNAME=_ElecEw
> -DVDWNAME=_VdwLJ -DCENTRAL=22 -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8
> -DNBNXN_GPU_CLUSTER_SIZE=8 -DNBNXN_GPU_JGROUP_SIZE=4
> -DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=4 -DNBNXN_MIN_RSQ=3.82e-07f
> -DIATYPE_SHMEM -cl-fast-relaxed-math
> -I/Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl
>
>

> --LOG START---
>
> :80:10: fatal error: 'nbnxn_ocl_kernel_pruneonly.clh' file
> not found
>
> #include "nbnxn_ocl_kernel_pruneonly.clh"
>
>  ^
>

Yet somehow this file was not found shortly afterwards. It's clearly being
told to look in the right place (from the -I flag in the build options).
That looks to me like an issue in the OpenCL driver / runtime. I see you're
using the latest Mac version, but perhaps trying to update the OpenCL
things will help with a more stable setup.

Mark

---LOG END
>
>
> ---
>
> Program: mdrun-test, version 2018-rc1-dev-20180103-871f2f460-unknown
>
> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 502)
>
> Function:cl_program gmx::ocl::compileProgram(FILE *, const std::string
> &, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
>
>
> Internal error (bug):
>
> Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 560 Compute Engine
>
>   Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE
>
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
> ---
>
>
>   Start 33: MdrunMpiTests
>
> 33/39 Test #33: MdrunMpiTests    Passed2.69 sec
>
>   Start 34: regressiontests/simple
>
> 34/39 Test #34: regressiontests/simple ...   Passed2.33 sec
>
>   Start 35: regressiontests/complex
>
> 35/39 Test #35: regressiontests/complex ..   Passed   53.42 sec
>
>   Start 36: regressiontests/kernel
>
> 36/39 Test #36: regressiontests/kernel ...   Passed   32.33 sec
>
>   Start 37: regressiontests/freeenergy
>
> 37/39 Test #37: regressiontests/freeenergy ...   Passed5.70 sec
>
>   Start 38: regressiontests/pdb2gmx
>
> 38/39 Test #38: regressiontests/pdb2gmx ..   Passed   15.66 sec
>
>   Start 39: regressiontests/rotation
>
> 39/39 Test #39: regressiontests/rotation .   Passed3.10 sec
>
>
> 97% tests passed, 1 tests failed out of 39
>
>
> Label Time Summary:
>
> GTest  =  19.86 sec*proc (33 tests)
>
> IntegrationTest=  18.38 sec*proc (3 tests)
>
> MpiTest=   2.73 sec*proc (3 tests)
>
> UnitTest   =   1.48 sec*proc (30 tests)
>
>
> Total Test time (real) = 132.48 sec
>
>
> The following tests FAILED:
>
> 32 - MdrunTests (Failed)
>
> Errors while running CTest
>
> make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
>
> make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
>
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
>
> make: *** [check] Error 2
>
>
>
>
> On Wed, Jan 3, 2018 at 7:42 PM, Yongchul Chung 
> wrote:
>
> > Thanks, I have successfully installed the release-2018 version of GROMACS
> > on Macbook Pro 2017 HighSierra.
> >
> >
> > On Tue, Jan 2, 2018 at 1:43 PM, Mark Abraham 
> > wrote:
> >
> >> Hi,
> >>
> >> Thanks, we have found and prepared a fix for an issue that looks very
> >> similar (https://gerrit.gromacs.org/#/c/7400). Apparently the Mac
>