[gmx-users] Compiling gromacs 4.6.5 on cray XT5m

[Gmx QA]

Dear users

I am having problems compiling gromacs 4.6.5 on a (rather ancient) Cray
XT5m machine.

My approach has been the following, but it stops during the make stage when
processing fftw.

1. Download gromacs-4.6.5 tar ball
tar -xvg gromacs-4.6.5.tar
cd gromacs-4.6.5
mkdir build
cd build

Then swap some modules
module swap PrgEnv-pgi PrgEnv-gnu
module swap gcc/4.4.4 gcc/4.6.1

I now have the following modules loaded:

~/gromacs-4.6.5/build> module list
Currently Loaded Modulefiles:
  1) modules/3.2.6.6
  2) portals/2.2.0-1.0301.26633.6.9.ss
  3) nodestat/2.2-1.0301.25918.4.1.ss
  4) sdb/1.0-1.0301.25929.4.88.ss
  5) MySQL/5.0.64-1.0301.2899.20.1.ss
  6)
lustre-cray_ss_s/1.8.4_2.6.27.48_0.12.1_1.0301.5943.18.1-1.0301.27524.1.24
  7) Base-opts/1.0.2-1.0301.25878.4.1.ss
  8) xtpe-network-seastar
  9) PrgEnv-gnu/3.1.72
 10) atp/1.4.4
 11) xt-asyncpe/5.10
 12) pmi/2.1.4-1..8596.15.1.ss
 13) xt-mpich2/5.3.5
 14) xt-libsci/10.5.02
 15) gcc/4.6.1

Then my cmake line is:
cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON  -DGMX_PREFER_STATIC_LIBS=ON
 -DBUILD_SHARED_LIBS=OFF -DCMAKE_INCLUDE_PATH=/opt/fftw/
3.3.0.0/x86_64/include/ -DCMAKE_LIBRARY_PATH=/opt/fftw/3.3.0.0/x86_64/lib/

Which proceeds fine through the configuring stage, but then during make I
get this:


-- Performing Test GNU_SSE2_CFLAG
-- Performing Test GNU_SSE2_CFLAG - Success
-- Looking for emmintrin.h
-- Looking for emmintrin.h - found
-- Enabling SSE2 Gromacs acceleration
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")
-- checking for module 'fftw3f'
--   package 'fftw3f' not found
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_r2r_1d in /opt/fftw/
3.3.0.0/x86_64/lib/fftw3f.so;/usr/lib/libm.so
-- Looking for fftwf_plan_r2r_1d in /opt/fftw/
3.3.0.0/x86_64/lib/fftw3f.so;/usr/lib/libm.so - not found
CMake Error at cmake/FindFFTW.cmake:97 (message):
  Could not find fftwf_plan_r2r_1d in
  /opt/fftw/3.3.0.0/x86_64/lib/fftw3f.so;/usr/lib/libm.so, take a look at
the
  error message in
  /home/users/pela3247/gromacs-4.6.5/build/CMakeFiles/CMakeError.log to find
  out what went wrong.  If you are using a static lib (.a) make sure you
have
  specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
  -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
  CMakeLists.txt:895 (find_package)


-- Configuring incomplete, errors occurred!


Clearly there is something screwy with fftw, but I am not experienced
enough with cray to tell what it is. Trying to do what the message suggest
(adding -DFFTWF_LIBRARY=''') only results in exactly the same error.

Could you please provide some pointers to where I go wrong?

Thanks
/PK
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Re: [gmx-users] Citing gromacs tools

[rajat desikan]

Thank you for the clarification, Prof. David.

On Tuesday, May 13, 2014, David van der Spoel  wrote:

> On 2014-05-13 07:52, rajat desikan wrote:
>
>> Hi All,
>> In many papers, the authors cite the main gromacs paper and simply declare
>> in the methods section that they used the gromacs analysis suite. Is that
>> a
>> good practice or should each tool be cited separately?
>>
>> Eg: g_sas says:
>>
>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
>> Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander
>> and
>> Michael Scharf
>> The Double Cube Lattice Method: Efficient Approaches to Numerical
>> Integration
>> of Surface Area and Volume and to Dot Surface Contouring of Molecular
>> Assemblies
>> J. Comp. Chem. 16 (1995) pp. 273-284
>>   --- Thank You ---  
>>
>>  Thanks for asking. It is good practice to cite specific algorithms if
> they are available. In this particular case referees of your paper might
> (and should!) demand that as well. To make this easier gromacs tools print
> relevant references. You citing those papers also helps developers.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> 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.
>


-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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[gmx-users] topol_pope.top

[Balasubramanian Suriyanarayanan]

Dear Sir, If am using POPE model for simulation , where we have the access
of p topol_pope.top.

regards

-- 
B.Suriyanarayanan
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Re: [gmx-users] Compiling gromacs 4.6.5 on cray XT5m

[Gmx QA]

Hello again

Problem solved, I think. At least it's compiling now. I downloaded fftw
myself and built it with --enable-static --disable-fortran, and that seems
to have worked.

Thanks
/PK



2014-05-13 9:06 GMT+02:00 Gmx QA :

> Dear users
>
> I am having problems compiling gromacs 4.6.5 on a (rather ancient) Cray
> XT5m machine.
>
> My approach has been the following, but it stops during the make stage
> when processing fftw.
>
> 1. Download gromacs-4.6.5 tar ball
> tar -xvg gromacs-4.6.5.tar
> cd gromacs-4.6.5
> mkdir build
> cd build
>
> Then swap some modules
> module swap PrgEnv-pgi PrgEnv-gnu
> module swap gcc/4.4.4 gcc/4.6.1
>
> I now have the following modules loaded:
>
> ~/gromacs-4.6.5/build> module list
> Currently Loaded Modulefiles:
>   1) modules/3.2.6.6
>   2) portals/2.2.0-1.0301.26633.6.9.ss
>   3) nodestat/2.2-1.0301.25918.4.1.ss
>   4) sdb/1.0-1.0301.25929.4.88.ss
>   5) MySQL/5.0.64-1.0301.2899.20.1.ss
>   6)
> lustre-cray_ss_s/1.8.4_2.6.27.48_0.12.1_1.0301.5943.18.1-1.0301.27524.1.24
>   7) Base-opts/1.0.2-1.0301.25878.4.1.ss
>   8) xtpe-network-seastar
>   9) PrgEnv-gnu/3.1.72
>  10) atp/1.4.4
>  11) xt-asyncpe/5.10
>  12) pmi/2.1.4-1..8596.15.1.ss
>  13) xt-mpich2/5.3.5
>  14) xt-libsci/10.5.02
>  15) gcc/4.6.1
>
> Then my cmake line is:
> cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON  -DGMX_PREFER_STATIC_LIBS=ON
>  -DBUILD_SHARED_LIBS=OFF -DCMAKE_INCLUDE_PATH=/opt/fftw/
> 3.3.0.0/x86_64/include/ -DCMAKE_LIBRARY_PATH=/opt/fftw/3.3.0.0/x86_64/lib/
>
> Which proceeds fine through the configuring stage, but then during make I
> get this:
>
> 
> -- Performing Test GNU_SSE2_CFLAG
> -- Performing Test GNU_SSE2_CFLAG - Success
> -- Looking for emmintrin.h
> -- Looking for emmintrin.h - found
> -- Enabling SSE2 Gromacs acceleration
> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")
> -- checking for module 'fftw3f'
> --   package 'fftw3f' not found
> -- pkg-config could not detect fftw3f, trying generic detection
> -- Looking for fftwf_plan_r2r_1d in /opt/fftw/
> 3.3.0.0/x86_64/lib/fftw3f.so;/usr/lib/libm.so
> -- Looking for fftwf_plan_r2r_1d in /opt/fftw/
> 3.3.0.0/x86_64/lib/fftw3f.so;/usr/lib/libm.so - not found
> CMake Error at cmake/FindFFTW.cmake:97 (message):
>   Could not find fftwf_plan_r2r_1d in
>   /opt/fftw/3.3.0.0/x86_64/lib/fftw3f.so;/usr/lib/libm.so, take a look at
> the
>   error message in
>   /home/users/pela3247/gromacs-4.6.5/build/CMakeFiles/CMakeError.log to
> find
>   out what went wrong.  If you are using a static lib (.a) make sure you
> have
>   specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
>   -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
> Call Stack (most recent call first):
>   CMakeLists.txt:895 (find_package)
>
>
> -- Configuring incomplete, errors occurred!
>
>
> Clearly there is something screwy with fftw, but I am not experienced
> enough with cray to tell what it is. Trying to do what the message suggest
> (adding -DFFTWF_LIBRARY=''') only results in exactly the same error.
>
> Could you please provide some pointers to where I go wrong?
>
> Thanks
> /PK
>
>
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[gmx-users] Regarding calculation of energy auto-correlation function

[Ravi Kumar Venkatraman]

Dear Gromacs User's,
Could anybody tell me how to calculate
energy auto-correlation function of the solvent from MDS trajectory of a
production run. I tried using g_energy_d option but it didn't work
properly, maybe I made a mistake in the commands. Following is the command
I have used,
 g_energy_d -f prodacn.edr -s prodacn.tpr -fluc -o energy.xvg
After executing the above command line, it opens a interactive window like
Pressure, temp ... etc. and I have chosen Total Energy as an option.

Please let me know if anybody know the solution for the above problem.

Thank you in advance
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[gmx-users] Simulating protein peptide complex

[Ruben Cloete]

Hi, Justin regarding protein peptide simulation do i prepare the peptide 
as i would a ligand (PRODRG) and add topology to .gro file?


Is there a tutorial for protein protein simulation?

Hope you can assist

Best regards
Ruben


On 26/04/2014 14:50, Justin Lemkul wrote:



On 4/26/14, 8:42 AM, Andrew Bostick wrote:

Dear Justin

Thanks for your reply.


This problem can be solved by changing the parameters related to file 
system

?



Well, you could, but that would require reformatting your file system 
for something that can handle file size > 2 GB.




If I add another RAM to my computer system, my problem solves?



No.

The simplest solutions are what I stated before - reduce your output 
volume or conduct your runs in shorter intervals of time. This is a 
very easy limitation to overcome, given the ability to concatenate the 
output later (obviously on a different machine that supports larger 
files).


-Justin



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[gmx-users] GPU not found

[Albert]

Hello:

I compiled Gromacs in a GPU machine with two GTX780Ti with following
command:

env CC=icc F77=ifort CXX=icpc
CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/intel/impi/
4.1.3.049/intel64:/soft/intel/mkl/lib/intel64 cmake ..
-DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
-DCMAKE_INSTALL_PREFIX=/soft/gromacs-5.0rc1 -DGMX_MPI=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda


however, when I try to run some jobs, it failed with messages:


NOTE: Error occurred during GPU detection:
  no CUDA-capable device is detected
  Can not use GPU acceleration, will fall back to CPU kernels.

Reading file 4.tpr, VERSION 4.6.5 (single precision)
Using 1 MPI process
Using 20 OpenMP threads


thank you very much.

ALbert
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Re: [gmx-users] GPU not found

[Mirco Wahab]

On 13.05.2014 11:18, Albert wrote:

I compiled Gromacs in a GPU machine with two GTX780Ti with following
command:

env CC=icc F77=ifort CXX=icpc
CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/intel/impi/
4.1.3.049/intel64:/soft/intel/mkl/lib/intel64 cmake ..
-DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
-DCMAKE_INSTALL_PREFIX=/soft/gromacs-5.0rc1 -DGMX_MPI=ON -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda

however, when I try to run some jobs, it failed with messages:


NOTE: Error occurred during GPU detection:
   no CUDA-capable device is detected
   Can not use GPU acceleration, will fall back to CPU kernels.


What does

$> nvidia-smi

on this machine print out?
see: 
http://manpages.ubuntu.com/manpages/natty/man1/alt-nvidia-current-smi.1.html


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Re: [gmx-users] GPU not found

[Albert]

Hello:

thx for reply.

it is very strange, I cannot run this command as normal user:

Failed to initialize NVML: Insufficient Permissions

here is the output I use sudo to run the command you mentioned:

+--+

| NVIDIA-SMI 331.67 Driver Version: 331.67
|
|---+--+--+
| GPU  NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr.
ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
M. |
|===+==+==|
|   0  GeForce GTX 780 Ti  Off  | :01:00.0 N/A |
N/A |
| 38%   42C  N/A N/A /  N/A | 10MiB /  3071MiB | N/A
Default |
+---+--+--+
|   1  GeForce GTX 780 Ti  Off  | :02:00.0 N/A |
N/A |
|  0%   34C  N/A N/A /  N/A | 10MiB /  3071MiB | N/A
Default |
+---+--+--+


+-+
| Compute processes:   GPU
Memory |
|  GPU   PID  Process name
Usage  |
|=|
|0Not
Supported   |
|1Not
Supported   |
+-+



2014-05-13 11:54 GMT+02:00 Mirco Wahab :

> On 13.05.2014 11:18, Albert wrote:
>
>> I compiled Gromacs in a GPU machine with two GTX780Ti with following
>> command:
>>
>> env CC=icc F77=ifort CXX=icpc
>> CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/intel/impi/
>> 4.1.3.049/intel64:/soft/intel/mkl/lib/intel64 cmake ..
>> -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
>> -DCMAKE_INSTALL_PREFIX=/soft/gromacs-5.0rc1 -DGMX_MPI=ON -DGMX_GPU=ON
>> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
>>
>> however, when I try to run some jobs, it failed with messages:
>>
>>
>> NOTE: Error occurred during GPU detection:
>>no CUDA-capable device is detected
>>Can not use GPU acceleration, will fall back to CPU kernels.
>>
>>  What does
>
> $> nvidia-smi
>
> on this machine print out?
> see: http://manpages.ubuntu.com/manpages/natty/man1/alt-
> nvidia-current-smi.1.html
>
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Re: [gmx-users] GPU not found

[Mirco Wahab]

On 13.05.2014 12:00, Albert wrote:

Hello:

thx for reply.
it is very strange, I cannot run this command as normal user:
Failed to initialize NVML: Insufficient Permissions
here is the output I use sudo to run the command you mentioned:


Please look into the solutions posted here:
http://stackoverflow.com/questions/13054262/cuda-runtime-api-error-38-no-cuda-capable-device-is-detected

Otherwise, I usually exec the following script on headless
nodes to get all the nvidia-devices user-accessible:

--- 8< --- [cut here: cudainit.sh ] 

#!/bin/sh
if [ "$?" -eq 0 ]; then
  # Count the number of NVIDIA controllers found.
  N3D=`/sbin/lspci | grep -i NVIDIA | grep "3D controller" | wc -l`
  NVGA=`/sbin/lspci | grep -i NVIDIA | grep "VGA compatible controller"
  wc -l`

  N=`expr $N3D + $NVGA - 1`

  for i in `seq 0 $N`; do
mknod -m 666 /dev/nvidia$i c 195 $i;
  done

  mknod -m 666 /dev/nvidiactl c 195 255
else
  exit 1
fi

--- 8< --- [cut here: cudainit.sh ] 

(run as root). This is not always necessary, seems to
depend on CUDA vs. driver version vs operating system
taste.

Regards

M.

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Re: [gmx-users] Can't make links on GROMACS

[Ly Minh Nhat]

@Justin: why does it remove?
@Chandan: I did use sudo when make links.

Off topic question: if I disable mail delivery but still keep subcribe the
mail list, will I receive your answer to my mail?

Thank you.


On Wed, May 7, 2014 at 7:05 PM, Justin Lemkul  wrote:

>
>
> On 5/7/14, 2:04 AM, Ooker wrote:
>
>> Hi, GROMACS' developers and users
>>
>> I am helped in this thread: https://www.mail-archive.com/
>> gromacs.org_gmx-users@maillist.sys.kth.se/msg02716.html[1]. Things is
>> good, however everytime I
>>
>> start a new bash shell, I have to use source
>> /usr/local/gromacs/bin/GMXRC, it's
>> annoying. I have tried reinstall GROMACS with sudo make links but there
>> is an error:
>>
>> ooker@ooker-Aspire-4741:~/gromacs-4.6.5/build$ sudo make links
>> make: *** No rule to make target `links'.  Stop.
>> I have tried
>> ln -s /usr/local/gromacs/bin/GMXRC /usr/local/bin/GMXRC
>> or add alias gxmrc to ~./bashrc but they are still useless. What should I
>> do?
>>
>>
> Just add
>
> source /usr/local/gromacs/bin/GMXRC
>
> to your .bashrc and it will be executed every time you open a new shell.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] GPU not found

[Albert]

Now the problem solved now after I reinstall NVIDIA driver. When I run in
single GPU, it works fine. However, when I try to run :

mpirun -np 2 mdrun_mpi -s test.tpr

it failed with messages:
[mpiexec@cudaA.compuBio] HYDU_getfullhostname
(./utils/others/others.c:136): getaddrinfo error (hostname: cudaA.compuBio,
error: Name or service not known)
[mpiexec@cudaA.compuBio] HYDU_sock_create_and_listen_portstr
(./utils/sock/sock.c:999): unable to get local hostname
[mpiexec@cudaA.compuBio] HYD_pmci_launch_procs
(./pm/pmiserv/pmiserv_pmci.c:313): unable to create PMI port
[mpiexec@cudaA.compuBio] main (./ui/mpich/mpiexec.c:877): process manager
returned error launching processes



I am using intel mpi...

thank you very much.

Albert



2014-05-13 11:54 GMT+02:00 Mirco Wahab :

> On 13.05.2014 11:18, Albert wrote:
>
>> I compiled Gromacs in a GPU machine with two GTX780Ti with following
>> command:
>>
>> env CC=icc F77=ifort CXX=icpc
>> CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/intel/impi/
>> 4.1.3.049/intel64:/soft/intel/mkl/lib/intel64 cmake ..
>> -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
>> -DCMAKE_INSTALL_PREFIX=/soft/gromacs-5.0rc1 -DGMX_MPI=ON -DGMX_GPU=ON
>> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
>>
>> however, when I try to run some jobs, it failed with messages:
>>
>>
>> NOTE: Error occurred during GPU detection:
>>no CUDA-capable device is detected
>>Can not use GPU acceleration, will fall back to CPU kernels.
>>
>>  What does
>
> $> nvidia-smi
>
> on this machine print out?
> see: http://manpages.ubuntu.com/manpages/natty/man1/alt-
> nvidia-current-smi.1.html
>
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Re: [gmx-users] GPU not found

[Mirco Wahab]

On 13.05.2014 12:42, Albert wrote:

Now the problem solved now after I reinstall NVIDIA driver. When I run in
single GPU, it works fine. However, when I try to run :

mpirun -np 2 mdrun_mpi -s test.tpr

it failed with messages:
[mpiexec@cudaA.compuBio] HYDU_getfullhostname
(./utils/others/others.c:136): getaddrinfo error (hostname: cudaA.compuBio,
error: Name or service not known)
[mpiexec@cudaA.compuBio] HYDU_sock_create_and_listen_portstr
(./utils/sock/sock.c:999): unable to get local hostname
[mpiexec@cudaA.compuBio] HYD_pmci_launch_procs
(./pm/pmiserv/pmiserv_pmci.c:313): unable to create PMI port
[mpiexec@cudaA.compuBio] main (./ui/mpich/mpiexec.c:877): process manager
returned error launching processes


I'm not familiar with Intel MPI.
(Why do you see importance in using the Intel tools at all?)

But on OpenMPI, there would be a cmd line option
specifying the host where the processes are
supposed to run on. I'm sure there is an equiv.
option with the Intel suite.

What is the output of
$> echo `hostname`

Is the MPI using ssh or rsh? Can the
machine ssh/rsh into itself? By using
which hostname?

Regards

M.

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[gmx-users] g_cluster: treating identical molecules as interchangeable

[Gil Rutter]

Hi all,

In a simulation of, say, 2 units of the same molecule, it would be useful
if g_cluster could treat the two molecules as being interchangeable.

For example, if molecule A has three atoms at coordinates C1, C2 and C3,
and identical molecule B has three atoms at coordinates C4, C5 and C6, this
frame would be clustered with a second frame in which molecule B is at C1,
C2 and C3 and molecule A is at C4, C5 and C6. (Indeed, in this case the
RMSD would be 0.)

Hopefully that makes sense. Is there any way to achieve this in g_cluster?

Best regards,

Gil Rutter
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Re: [gmx-users] Simulating protein peptide complex

[Justin Lemkul]

On 5/13/14, 4:30 AM, Ruben Cloete wrote:

Hi, Justin regarding protein peptide simulation do i prepare the peptide as i
would a ligand (PRODRG) and add topology to .gro file?



No, just run it through pdb2gmx.


Is there a tutorial for protein protein simulation?



No, because it's not really different from any other protein-in-water system.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] Can't make links on GROMACS

[Justin Lemkul]

On 5/13/14, 6:39 AM, Ly Minh Nhat wrote:

@Justin: why does it remove?


At present, it doesn't really make sense.  In 5.0-rc1, all the tools are simply 
links to a binary called gmx that executes all of the programs, so linking to 
links is really not convenient.



@Chandan: I did use sudo when make links.

Off topic question: if I disable mail delivery but still keep subcribe the
mail list, will I receive your answer to my mail?



If you're disabling delivery, probably not.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Positive energy .

[sujithkakkat .]

Dear all,

I am running simulations for a water-CO2 system using the OPLSAA
forcefield, where I use TIP4P/Ice water model and the EPM2 model for CO2.
After energy minimization I found the value of potential energy to be
positive, and also the maximum force value was high (I requested Fmax <10
). The values are as follows;

Potential Energy=  1.7600962e+05
Maximum force =  6.5140656e+01 on atom 1176
Norm of force=  8.7009411e+00

Earlier when I did a simulation for gaseous CO2 using the same model, the
potential energies were always positive. But I doubt whether the energy can
be positive here.

I want to make sure that I am not using any wrong parameters, before I
proceed. Please comment.




  My MDP file is as given below;

; Run control
integrator = steep
nsteps = 2

; EM criteria and other stuff
emtol = 10
emstep   = 0.01
niter= 20
nbfgscorr = 10

; Output control
nstlog   = 1
nstenergy = 1

; Neighborsearching and short-range nonbonded interactions
nstlist= 1
ns_type = grid
pbc   = xyz
rlist   = 1.0

; Electrostatics

coulombtype = PME
rcoulomb  = 1.0

; van der Waals

vdw-type = switch
rvdw-switch =0.8
rvdw   = 0.9

; Apply long range dispersion corrections for Energy and Pressure

DispCorr = EnerPres

; Spacing for the PME/PPPM FFT grid

fourierspacing = 0.12

; EWALD/PME/PPPM parameters

pme_order = 6
ewald_rtol  = 1e-06
epsilon_surface  = 0
optimize_fft= no

; Temperature and pressure coupling are off during EM

tcoupl  = no
pcoupl = no

; Generate velocities to start

gen_vel = no

; options for bonds

constraints = all-bonds

; Type of constraint algorithm

constraint-algorithm = lincs

; Do not constrain the starting configuration

continuation = no

; Highest order in the expansion of the constraint coupling matrix

lincs-order = 12
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Re: [gmx-users] g_cluster: treating identical molecules as interchangeable

[Mark Abraham]

Hi,

I would expect there is no way to do this with g_cluster. g_cluster -h
should mention it if it did exist. The only way to implement it is to
iterate over all permutations of equivalent molecules. That's doable, but
it would have to have been implemented deliberately.

Mark


On Tue, May 13, 2014 at 1:27 PM, Gil Rutter wrote:

> Hi all,
>
> In a simulation of, say, 2 units of the same molecule, it would be useful
> if g_cluster could treat the two molecules as being interchangeable.
>
> For example, if molecule A has three atoms at coordinates C1, C2 and C3,
> and identical molecule B has three atoms at coordinates C4, C5 and C6, this
> frame would be clustered with a second frame in which molecule B is at C1,
> C2 and C3 and molecule A is at C4, C5 and C6. (Indeed, in this case the
> RMSD would be 0.)
>
> Hopefully that makes sense. Is there any way to achieve this in g_cluster?
>
> Best regards,
>
> Gil Rutter
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Re: [gmx-users] npt dynamics generate a lot of pdb files

[Natalia Alveal F.]

But, I modify nstlist only for 500 ps to fix the problem that comming from
NVT. After that, I change nstlist to default value for MD.
Natalia


2014-05-08 12:51 GMT-04:00 Mark Abraham :

> By modifying nstlist, you're very likely fixing a symptom, rather than
> fixing the problem.
>
> Mark
>
>
> On Thu, May 8, 2014 at 6:21 PM, Natalia Alveal F.  >wrote:
>
> > Dear Gromacs users,
> > Reducing the nstlist value works for me.
> >
> > Thanks a lot for yours suggestions.
> >
> >
> > 2014-05-06 22:47 GMT-04:00 Justin Lemkul :
> >
> > >
> > >
> > > On 5/6/14, 5:23 PM, Riccardo Concu wrote:
> > >
> > >> Dear Natalia,
> > >> that error basicly means your system is not well equilibrated, or it
> is
> > >> exploading and so on. Normally, reducing the nstlist value in your mdp
> > >> file
> > >> should work.
> > >>
> > >
> > > Usually there are far more catastrophic problems than nstlist, and the
> > > only case I've found where anything improves is during EM where nstlist
> > > must be 1. Decreasing the value may work, but I would be very
> surprised,
> > > and ultimately there is a price to be paid in terms of performance that
> > may
> > > not be necessary.
> > >
> > > The OP should post a full description of prior minimization and
> > > equilibration as well as the full .mdp file for the crashing run.
> >  Without
> > > that information, it's totally guesswork as to what's going on.
> > >
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
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> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Natalia Alveal Fuentealba
> > Ingeniera en Bioinformática
> > Laboratory of Membranes Proteins Structure and Signalling
> > Departamento de Fisiología
> > Pontificia Universidad Católica de Chile
> > Alameda 340, Santiago, Chile
> > Fono: 56-2-3542877
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-- 
Natalia Alveal Fuentealba
Ingeniera en Bioinformática
Laboratory of Membranes Proteins Structure and Signalling
Departamento de Fisiología
Pontificia Universidad Católica de Chile
Alameda 340, Santiago, Chile
Fono: 56-2-3542877
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Re: [gmx-users] g_cluster: treating identical molecules as interchangeable

[Erik Marklund]

Hi,

If you have a small number of identical molecules you can achieve something 
along those lines by creating a trajectory where, say, the first half is the 
coordinates of the first molecule and the second half is the coordinated of the 
second molecule (for the case of two identical molecules). No matter the way 
you go about it there is no avoiding getting some artificial contribution to 
the transition probabilities between clusters.

Erik

Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 13 May 2014, at 14:57, Mark Abraham  wrote:

> Hi,
> 
> I would expect there is no way to do this with g_cluster. g_cluster -h
> should mention it if it did exist. The only way to implement it is to
> iterate over all permutations of equivalent molecules. That's doable, but
> it would have to have been implemented deliberately.
> 
> Mark
> 
> 
> On Tue, May 13, 2014 at 1:27 PM, Gil Rutter wrote:
> 
>> Hi all,
>> 
>> In a simulation of, say, 2 units of the same molecule, it would be useful
>> if g_cluster could treat the two molecules as being interchangeable.
>> 
>> For example, if molecule A has three atoms at coordinates C1, C2 and C3,
>> and identical molecule B has three atoms at coordinates C4, C5 and C6, this
>> frame would be clustered with a second frame in which molecule B is at C1,
>> C2 and C3 and molecule A is at C4, C5 and C6. (Indeed, in this case the
>> RMSD would be 0.)
>> 
>> Hopefully that makes sense. Is there any way to achieve this in g_cluster?
>> 
>> Best regards,
>> 
>> Gil Rutter
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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Re: [gmx-users] Simulations in NVE ensemble with CHARMM36 - update

[ABEL Stephane 175950]

Hello Justin

Thanks for your reply. I have finally found why I obtained a large drift and 
decrease of the temp of my system during the NVE : I stupidly mixed different 
cpt and tpr files. If I use the right files and the following parameters below 
suggested by M. Shirts in  [1] for my tests:

rlist   = 1.3
;vdW
vdwtype = Switch
rvdw= 1.1
rvdw_switch = 1.0

; Electrostatics
coulombtype = PME
rcoulomb= 1.3

The energy and the temp of my system remain stable during the 100 ps of my 
simulation after  initial small decrease of the energy and the temp to 295.5 K 
(initial temp was 297.904 K)

[1] http://comments.gmane.org/gmane.science.biology.gromacs.user/42686

Please also note that with the parameters for Verlet options you gave I obtain 
the following error with 4.6.5 for simulations with NVE, 

 Temperature coupling is required for calculating rlist using the energy
  drift with verlet-buffer-drift > 0. Either use temperature coupling or
  set rlist yourself together with verlet-buffer-drift = -1

If I add the verlet-buffer-drift = -1 option in my mdp (not sure it is 
correct), grompp gives only two notes 

NOTE 1 [file run_CH_1_NVE_pot_mod.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.


NOTE 2 [file run_CH_1_NVE_pot_mod.mdp]:
  rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
  buffer. The cluster pair list does have a buffering effect, but choosing
  a larger rlist might be necessary for good energy conservation.


Stéphane


On 5/7/14, 9:05 AM, ABEL Stephane 175950 wrote:
> Dear GMX-users
>
> I have done a 90 ns long simulation of a heterogeneous  system (SPCE water, 
> phospholipids and a hydrophobic solvent) in NPT ensemble (298 K at 1 bar) 
> with GROMACS4.6.5. to compute related dynamical properties, I would like to 
> continue this simulation in NVE. But I am puzzled to choose the mdp 
> parameters to have a good energy conservation. Indeed, I have checked the 
> gromacs 2004 JCTC or the following and follow the advices given in the 
> following threads
>
> http://comments.gmane.org/gmane.science.biology.gromacs.user/42686
> https://www.mail-archive.com/gmx-users@gromacs.org/msg60393.html
>
> But I always obtain for my system a large drift and the temp decreases 
> significantly (20 K) after few dozens of ps (the initial temp was around 
> 297.3 K). For this simulation I used the double precision of gromacs with a 
> timestep of 1 fs.
>

Can you provide a full .mdp file so we can look at all your settings?  Are these
drifts during NPT or NVE?

> More, since I have never used the potential-modifier features, so I not sure 
> how to setup  the correct parameters in the context of CHARMM simulations.
>

With the caveat that I have NOT thoroughly tested the following, my
understanding of the new Verlet options indicates that these settings should
perform pretty well using CHARMM36:

cutoff-scheme = Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = Potential-switch
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2

Again, barely tested on my part, and never tested for NVE.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Simulations in NVE ensemble with CHARMM36 - update

[Justin Lemkul]

On 5/13/14, 10:44 AM, ABEL Stephane 175950 wrote:

Hello Justin

Thanks for your reply. I have finally found why I obtained a large drift and 
decrease of the temp of my system during the NVE : I stupidly mixed different 
cpt and tpr files. If I use the right files and the following parameters below 
suggested by M. Shirts in  [1] for my tests:

rlist   = 1.3
;vdW
vdwtype = Switch
rvdw= 1.1
rvdw_switch = 1.0

; Electrostatics
coulombtype = PME
rcoulomb= 1.3



CHARMM parameters can be very sensitive to the value of rvdw.  It's something we 
consider as close to an absolute rule as you get, so the settings above should 
be modified to read:


rlist = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.4

Or use the settings in my previous message in version 5.0-rc1.


The energy and the temp of my system remain stable during the 100 ps of my 
simulation after  initial small decrease of the energy and the temp to 295.5 K 
(initial temp was 297.904 K)

[1] http://comments.gmane.org/gmane.science.biology.gromacs.user/42686

Please also note that with the parameters for Verlet options you gave I obtain 
the following error with 4.6.5 for simulations with NVE,

  Temperature coupling is required for calculating rlist using the energy
   drift with verlet-buffer-drift > 0. Either use temperature coupling or
   set rlist yourself together with verlet-buffer-drift = -1



Good to know; I've never had a need to run NVE.


If I add the verlet-buffer-drift = -1 option in my mdp (not sure it is 
correct), grompp gives only two notes

NOTE 1 [file run_CH_1_NVE_pot_mod.mdp]:
   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
   that with the Verlet scheme, nstlist has no effect on the accuracy of
   your simulation.


NOTE 2 [file run_CH_1_NVE_pot_mod.mdp]:
   rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
   buffer. The cluster pair list does have a buffering effect, but choosing
   a larger rlist might be necessary for good energy conservation.



I don't believe the options I provided will work in 4.6.5; they definitely 
should in 5.0-rc1, so a test with verlet-buffer-drift = -1 would be potentially 
useful.


-Justin



Stéphane


On 5/7/14, 9:05 AM, ABEL Stephane 175950 wrote:

Dear GMX-users

I have done a 90 ns long simulation of a heterogeneous  system (SPCE water, 
phospholipids and a hydrophobic solvent) in NPT ensemble (298 K at 1 bar) with 
GROMACS4.6.5. to compute related dynamical properties, I would like to continue 
this simulation in NVE. But I am puzzled to choose the mdp parameters to have a 
good energy conservation. Indeed, I have checked the gromacs 2004 JCTC or the 
following and follow the advices given in the following threads

http://comments.gmane.org/gmane.science.biology.gromacs.user/42686
https://www.mail-archive.com/gmx-users@gromacs.org/msg60393.html

But I always obtain for my system a large drift and the temp decreases 
significantly (20 K) after few dozens of ps (the initial temp was around 297.3 
K). For this simulation I used the double precision of gromacs with a timestep 
of 1 fs.



Can you provide a full .mdp file so we can look at all your settings?  Are these
drifts during NPT or NVE?


More, since I have never used the potential-modifier features, so I not sure 
how to setup  the correct parameters in the context of CHARMM simulations.



With the caveat that I have NOT thoroughly tested the following, my
understanding of the new Verlet options indicates that these settings should
perform pretty well using CHARMM36:

cutoff-scheme = Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = Potential-switch
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2

Again, barely tested on my part, and never tested for NVE.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Positive energy .

[Bryan Roessler]

Did you hit your nsteps limit? 2 probably isn't enough steps to get
below 10 Fmax.

*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
*uab.edu/cmdb *
Knowledge that will change your world


On Tue, May 13, 2014 at 8:30 AM, sujithkakkat . wrote:

> Dear all,
>
> I am running simulations for a water-CO2 system using the OPLSAA
> forcefield, where I use TIP4P/Ice water model and the EPM2 model for CO2.
> After energy minimization I found the value of potential energy to be
> positive, and also the maximum force value was high (I requested Fmax <10
> ). The values are as follows;
>
> Potential Energy=  1.7600962e+05
> Maximum force =  6.5140656e+01 on atom 1176
> Norm of force=  8.7009411e+00
>
> Earlier when I did a simulation for gaseous CO2 using the same model, the
> potential energies were always positive. But I doubt whether the energy can
> be positive here.
>
> I want to make sure that I am not using any wrong parameters, before I
> proceed. Please comment.
>
>
>
>
>   My MDP file is as given below;
>
> ; Run control
> integrator = steep
> nsteps = 2
>
> ; EM criteria and other stuff
> emtol = 10
> emstep   = 0.01
> niter= 20
> nbfgscorr = 10
>
> ; Output control
> nstlog   = 1
> nstenergy = 1
>
> ; Neighborsearching and short-range nonbonded interactions
> nstlist= 1
> ns_type = grid
> pbc   = xyz
> rlist   = 1.0
>
> ; Electrostatics
>
> coulombtype = PME
> rcoulomb  = 1.0
>
> ; van der Waals
>
> vdw-type = switch
> rvdw-switch =0.8
> rvdw   = 0.9
>
> ; Apply long range dispersion corrections for Energy and Pressure
>
> DispCorr = EnerPres
>
> ; Spacing for the PME/PPPM FFT grid
>
> fourierspacing = 0.12
>
> ; EWALD/PME/PPPM parameters
>
> pme_order = 6
> ewald_rtol  = 1e-06
> epsilon_surface  = 0
> optimize_fft= no
>
> ; Temperature and pressure coupling are off during EM
>
> tcoupl  = no
> pcoupl = no
>
> ; Generate velocities to start
>
> gen_vel = no
>
> ; options for bonds
>
> constraints = all-bonds
>
> ; Type of constraint algorithm
>
> constraint-algorithm = lincs
>
> ; Do not constrain the starting configuration
>
> continuation = no
>
> ; Highest order in the expansion of the constraint coupling matrix
>
> lincs-order = 12
> --
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] Positive energy .

[Rasoul Nasiri]

Why do you think positive values are doubtful?
What matters are energy differences between different snapshots
The absolute energy is meaningless in the FF framework.

Rasoul


On Tue, May 13, 2014 at 3:59 PM, Bryan Roessler  wrote:

> Did you hit your nsteps limit? 2 probably isn't enough steps to get
> below 10 Fmax.
>
> *Bryan Roessler | Graduate Research Assistant*
> UAB | The University of Alabama at Birmingham
> *uab.edu/cmdb *
> Knowledge that will change your world
>
>
> On Tue, May 13, 2014 at 8:30 AM, sujithkakkat .  >wrote:
>
> > Dear all,
> >
> > I am running simulations for a water-CO2 system using the OPLSAA
> > forcefield, where I use TIP4P/Ice water model and the EPM2 model for CO2.
> > After energy minimization I found the value of potential energy to be
> > positive, and also the maximum force value was high (I requested Fmax <10
> > ). The values are as follows;
> >
> > Potential Energy=  1.7600962e+05
> > Maximum force =  6.5140656e+01 on atom 1176
> > Norm of force=  8.7009411e+00
> >
> > Earlier when I did a simulation for gaseous CO2 using the same model, the
> > potential energies were always positive. But I doubt whether the energy
> can
> > be positive here.
> >
> > I want to make sure that I am not using any wrong parameters, before I
> > proceed. Please comment.
> >
> >
> >
> >
> >   My MDP file is as given below;
> >
> > ; Run control
> > integrator = steep
> > nsteps = 2
> >
> > ; EM criteria and other stuff
> > emtol = 10
> > emstep   = 0.01
> > niter= 20
> > nbfgscorr = 10
> >
> > ; Output control
> > nstlog   = 1
> > nstenergy = 1
> >
> > ; Neighborsearching and short-range nonbonded interactions
> > nstlist= 1
> > ns_type = grid
> > pbc   = xyz
> > rlist   = 1.0
> >
> > ; Electrostatics
> >
> > coulombtype = PME
> > rcoulomb  = 1.0
> >
> > ; van der Waals
> >
> > vdw-type = switch
> > rvdw-switch =0.8
> > rvdw   = 0.9
> >
> > ; Apply long range dispersion corrections for Energy and Pressure
> >
> > DispCorr = EnerPres
> >
> > ; Spacing for the PME/PPPM FFT grid
> >
> > fourierspacing = 0.12
> >
> > ; EWALD/PME/PPPM parameters
> >
> > pme_order = 6
> > ewald_rtol  = 1e-06
> > epsilon_surface  = 0
> > optimize_fft= no
> >
> > ; Temperature and pressure coupling are off during EM
> >
> > tcoupl  = no
> > pcoupl = no
> >
> > ; Generate velocities to start
> >
> > gen_vel = no
> >
> > ; options for bonds
> >
> > constraints = all-bonds
> >
> > ; Type of constraint algorithm
> >
> > constraint-algorithm = lincs
> >
> > ; Do not constrain the starting configuration
> >
> > continuation = no
> >
> > ; Highest order in the expansion of the constraint coupling matrix
> >
> > lincs-order = 12
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Re: [gmx-users] Positive energy .

[Justin Lemkul]

On 5/13/14, 11:21 AM, Rasoul Nasiri wrote:

Why do you think positive values are doubtful?
What matters are energy differences between different snapshots
The absolute energy is meaningless in the FF framework.



Not entirely true.  While the actual value itself is totally force 
field-dependent and is not a free energy, the fact that the OP is getting 
positive energies in the condensed phase is strange.  It means that the system 
is net-repulsive, which should not be the case, especially if it is solvated in 
water, in which hydrogen bonding should dominate.


Without more details about system size, .mdp settings, and force field details, 
it's hard to provide the OP with any real suggestions.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Can't make links on GROMACS

[Ooker]

Justin Lemkul  writes:

> 
> 
> On 5/13/14, 6:39 AM, Ly Minh Nhat wrote:
> >   Justin: why does it remove?
> 
> At present, it doesn't really make sense.  In 5.0-rc1, all the tools are
simply 
> links to a binary called gmx that executes all of the programs, so linking to 
> links is really not convenient.
> 
> >   Chandan: I did use sudo when make links.
> >
> > Off topic question: if I disable mail delivery but still keep subcribe the
> > mail list, will I receive your answer to my mail?
> >
> 
> If you're disabling delivery, probably not.
> 
> -Justin
> 
Just wonder, why don't Gromacs use Google Groups for mailing list? I have
found that it uses three different list: 
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/ (the
best one for me)
http://221.science-biology-gromacs-user.biotalk.us/ (slow update, can reply
by clicking button)
and https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ (the
ugliest, but referred from Gromacs website).

The way Google Groups sorts is intuitive, easy to reply.


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[gmx-users] Ion concentration of genion vs charmm-gui

[Ali Khan]

Hey,

I generated a membrane in charmm-gui that I will be simulating in gromacs.
I am using genion to add 0.14 M potassium by using the -conc flag. In a box
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui, the
server stated that I should add 232 potassium ions to reach a 0.14 M
concentration. Does anyone have a suggestion of which potassium ion number
I should go with?

Best Wishes,
Ali Khan
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Re: [gmx-users] Can't make links on GROMACS

[Mark Abraham]

On Tue, May 13, 2014 at 7:56 PM, Ooker  wrote:

> Justin Lemkul  writes:
>
> >
> >
> > On 5/13/14, 6:39 AM, Ly Minh Nhat wrote:
> > >   Justin: why does it remove?
> >
> > At present, it doesn't really make sense.  In 5.0-rc1, all the tools are
> simply
> > links to a binary called gmx that executes all of the programs, so
> linking to
> > links is really not convenient.
> >
> > >   Chandan: I did use sudo when make links.
> > >
> > > Off topic question: if I disable mail delivery but still keep subcribe
> the
> > > mail list, will I receive your answer to my mail?
> > >
> >
> > If you're disabling delivery, probably not.
> >
> > -Justin
> >
> Just wonder, why don't Gromacs use Google Groups for mailing list?


We'd be happy to use various platforms, but any change that requires
thousands of people to opt in is not worth the cost. Even if many
participants are read-only or inactive, it is valuable for the GROMACS team
when trying to attract funding to be able to point to a number of
mailing-list subscribers as one proxy for the number of people using
GROMACS. Switching to something other than mailman would only work if we
can port the subscriber list.

I have
> found that it uses three different list:
> https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/(the
> best one for me)
> http://221.science-biology-gromacs-user.biotalk.us/ (slow update, can
> reply
> by clicking button)
>

Those are run by third parties for whatever reason they have. I'm surprised
they are able to post at all.

Mark

and https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ (the
> ugliest, but referred from Gromacs website).
>
> The way Google Groups sorts is intuitive, easy to reply.
>
>
> --
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>
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] Ion concentration of genion vs charmm-gui

[Mark Abraham]

Sounds like a problem for a high-school chemistry test ;-) concentration =
quantity / volume. From the factor of ~1000, probably you're inputting box
sizes in A instead of nm, or vice-versa, somewhere.

Mark


On Tue, May 13, 2014 at 8:43 PM, Ali Khan  wrote:

> Hey,
>
> I generated a membrane in charmm-gui that I will be simulating in gromacs.
> I am using genion to add 0.14 M potassium by using the -conc flag. In a box
> with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
> should add 201 K atoms. When I constructed the system in charmm-gui, the
> server stated that I should add 232 potassium ions to reach a 0.14 M
> concentration. Does anyone have a suggestion of which potassium ion number
> I should go with?
>
> Best Wishes,
> Ali Khan
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] Ion concentration of genion vs charmm-gui

[Antonio Baptista]

Actually, your target concentration usually refers to the macroscopic 
solution bulk, not to the simulation box. Therefore, it is generally more 
correct to think in terms of the ion:solvent molar ratios -- that is, turn 
your molar concentration into the corresponding macroscopic ion:solvent 
molar ratios, and then use those ratios in your box.


In many cases it doesn't make much difference which approach you use, 
because the fraction of box volume occupied by the non-solvent part of the 
simulated system is often very small. However, a membrane typically 
occupies a substantial volume of your box, so I would advise the molar 
fraction approach in your case.


(Strictly speaking, not even that is necessarily correct, because your 
system of interest may induce a local ion concentration different from the 
bulk one. But that is an entirely different issue.)


Best,
Antonio


On Tue, 13 May 2014, Mark Abraham wrote:


Sounds like a problem for a high-school chemistry test ;-) concentration =
quantity / volume. From the factor of ~1000, probably you're inputting box
sizes in A instead of nm, or vice-versa, somewhere.

Mark


On Tue, May 13, 2014 at 8:43 PM, Ali Khan  wrote:


Hey,

I generated a membrane in charmm-gui that I will be simulating in gromacs.
I am using genion to add 0.14 M potassium by using the -conc flag. In a box
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui, the
server stated that I should add 232 potassium ions to reach a 0.14 M
concentration. Does anyone have a suggestion of which potassium ion number
I should go with?

Best Wishes,
Ali Khan
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--
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN, 2780-157 Oeiras, Portugal
phone: +351-214469619 email: bapti...@itqb.unl.pt
fax:   +351-214411277 WWW:   http://www.itqb.unl.pt/~baptista
--

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[gmx-users] quesion about MIC

[纪律部长 王海强]

Dear All,


I am a new user of gromacs, and I want to use gromacs on MIC.
Recently I see the gromacs-5.0beta2 published, and in the lists of rebision
changes, I see it has been added the SIMD supported for Intel MIC. 
But when  run the gromacs on MIC, it doesn't use the MIC card. 
On the other hand I didn't see any information in the source code about offload.
So I wonder that if I want to use the gromacs with MIC acceleration, how to 
configure and compile the gromacs and whether I need to change the source code 
myself.
Is there someone know the answer to the problem?


Thank you very much for your time.


regards
Haiqiang Wang




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Re: [gmx-users] quesion about MIC

[Christopher Neale]

I recall reading somewhere that MIC support is only native at this point. That 
is, you can run simulations entirely on MICs, but not hybrid CPU-MIC 
simulations. Don't recall where I read that and can't easily find it online. 

Chris.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of 纪律部长 王海强 

Sent: 13 May 2014 20:38
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] quesion about MIC

Dear All,


I am a new user of gromacs, and I want to use gromacs on MIC.
Recently I see the gromacs-5.0beta2 published, and in the lists of rebision
changes, I see it has been added the SIMD supported for Intel MIC.
But when  run the gromacs on MIC, it doesn't use the MIC card.
On the other hand I didn't see any information in the source code about offload.
So I wonder that if I want to use the gromacs with MIC acceleration, how to 
configure and compile the gromacs and whether I need to change the source code 
myself.
Is there someone know the answer to the problem?


Thank you very much for your time.


regards
Haiqiang Wang




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Re: [gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled

[Steven Neumann]

Thanks a lot! Berendsen barostat works well with V-rescale using REMD, no
crashes observed.


On Tue, May 13, 2014 at 2:08 PM, Mark Abraham wrote:

> On May 13, 2014 7:21 AM, "Steven Neumann"  wrote:
> >
> > Thanks a lot! So which combination of thermostat/barostat would provide a
> > proper ensemble without crashes?
>
> Various - but only P-R for the barostat in GROMACS, so you must be
> conservative with REMD exchange period. That will depend on the system and
> tau-p in a way that I expect nobody has studied. Hence avoiding NPT.
>
> > I am looking in the literature but did not
> > find anything.
>
> Some discussion in the manual.
>
> Mark
> >
> > On Tue, May 13, 2014 at 6:34 AM, Mark Abraham  >wrote:
> >
> > > I would generally encourage the use of NVT REMD. However, note that P-R
> > > does exhibit unstable oscillatory behaviour when not close to
> equilibrium.
> > > REMD is supposed to stay in equilibrium by design, but this gets double
> > > crossed if the exchange period is too short with respect to the
> > > autocorrelation of whatever is relevant, because a subsequent exchange
> is
> > > not from the right ensemble, so all bets are off.
> > >
> > > Mark
> > > On May 13, 2014 4:01 AM, "Steven Neumann" 
> wrote:
> > >
> > > > Or just to switch to NVT? I guess it would be less realistic if one
> wants
> > > > to study extract the most likely conformation...
> > > >
> > > >
> > > > On Tue, May 13, 2014 at 3:26 AM, Steven Neumann <
> s.neuman...@gmail.com
> > > > >wrote:
> > > >
> > > > > What would you recommend then? Equilibrate with Berendsen barostat
> and
> > > > > v-rescale thermostat?
> > > > >
> > > > >
> > > > > On Mon, May 12, 2014 at 2:01 PM, Justin Lemkul 
> > > wrote:
> > > > >
> > > > >>
> > > > >>
> > > > >> On 5/12/14, 3:58 AM, Steven Neumann wrote:
> > > > >>
> > > > >>> Dear Gmx Users,
> > > > >>>
> > > > >>> I am running REMD of a small protein in water. I have 36
> > > temperatures.
> > > > >>> After minimization I equilibrate each with nvt and npt ensemble.
> > > Then I
> > > > >>> start REMD with -multidir. The mdp:
> > > > >>>
> > > > >>>
> > > > >>> ; Run parameters
> > > > >>> integrator  = md; leap-frog integrator
> > > > >>> nsteps  = 5000
> > > > >>> dt  = 0.002 ; 2 fs
> > > > >>> ; Output control
> > > > >>> nstxout = 0   ; save coordinates every 0.2 ps
> > > > >>> nstvout = 0   ; save velocities every 0.2 ps
> > > > >>> nstenergy   = 5000   ; save energies every 0.2 ps
> > > > >>> nstxtcout   = 5000
> > > > >>> nstlog  = 5000
> > > > >>> ; Bond parameters
> > > > >>> continuation= no   ; first dynamics run
> > > > >>> constraint_algorithm = lincs; holoyesmic constraints
> > > > >>> constraints = all-bonds ; all bonds (even heavy atom-H
> bonds)
> > > > >>> constrained
> > > > >>> lincs_iter  = 1 ; accuracy of LINCS
> > > > >>> lincs_order = 4 ; also related to accuracy
> > > > >>> ; Neighborsearching
> > > > >>> ns_type = grid  ; search neighboring grid cells
> > > > >>> nstlist = 5 ; 10 fs
> > > > >>> vdwtype = Switch
> > > > >>> rvdw-switch = 1.0
> > > > >>> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
> > > > >>> rcoulomb= 1.4   ; short-range electrostatic cutoff (in
> nm)
> > > > >>> rvdw= 1.2   ; short-range van der Waals cutoff (in
> nm)
> > > > >>> ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted
> > > > >>> potential
> > > > >>> rcoulomb
> > > > >>> ; Electrostatics
> > > > >>> coulombtype = PME   ; Particle Mesh Ewald for long-range
> > > > >>> electrostatics
> > > > >>> pme_order   = 4 ; cubic interpolation
> > > > >>> fourierspacing  = 0.12  ; grid spacing for FFT
> > > > >>> ; Temperature coupling is on
> > > > >>> tcoupl  = V-rescale ; modified Berendsen
> > > > >>> thermostat
> > > > >>> tc_grps = Protein Water_and_ions   ; two coupling groups -
> more
> > > > >>> accurate
> > > > >>> tau_t   = 0.1   0.1 ; time constant, in
> ps
> > > > >>> ref_t   = 320.12   320.12 ; reference
> > > > >>> temperature,
> > > > >>> one for each group, in K
> > > > >>> ; Pressure coupling is on
> > > > >>> pcoupl  = Parrinello-Rahman ; pressure coupling
> is on
> > > > for
> > > > >>> NPT
> > > > >>> pcoupltype  = isotropic ; uniform scaling of
> box
> > > > >>> vectors
> > > > >>> tau_p   = 2.0   ; time constant, in
> ps
> > > > >>> ref_p   = 1.0   ; reference pressure,
> in
> > > > bar
> > > > >>> compressibility = 4.5e-5; isothermal
> > > > compressibility
> > > > >>> of
> > > > >>> water, bar^-1
> > > > >>> refcoord_scaling = com
> > > > >>> ; Periodic boundary conditions
> > > > >>> pbc = xyz   ; 3-D PBC
> > > > >>> gen_temp= 320.12
> > > > >>> DispCorr= EnerP

Re: [gmx-users] Ion concentration of genion vs charmm-gui

[Ali Khan]

Sorry Mark,

I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232 potassium
atoms. Its a small difference, and both methods have the same box size.


On Tue, May 13, 2014 at 3:38 PM, Mark Abraham wrote:

> Sounds like a problem for a high-school chemistry test ;-) concentration =
> quantity / volume. From the factor of ~1000, probably you're inputting box
> sizes in A instead of nm, or vice-versa, somewhere.
>
> Mark
>
>
> On Tue, May 13, 2014 at 8:43 PM, Ali Khan  wrote:
>
> > Hey,
> >
> > I generated a membrane in charmm-gui that I will be simulating in
> gromacs.
> > I am using genion to add 0.14 M potassium by using the -conc flag. In a
> box
> > with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
> > should add 201 K atoms. When I constructed the system in charmm-gui, the
> > server stated that I should add 232 potassium ions to reach a 0.14 M
> > concentration. Does anyone have a suggestion of which potassium ion
> number
> > I should go with?
> >
> > Best Wishes,
> > Ali Khan
> > --
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Re: [gmx-users] Positive energy .

[sujithkakkat .]

Hello Justin and others,

   Thank you for the response . Here are mode details of the system; ( in
the order ; MDP settings, itp  and top files) . The system consists of 460
water molecules and 1 CO2 molecule . I am trying to find the  free energy
of solvation for CO2 in water at various temperatures and pressure.

*MDP settings:*

; Run control
integrator = steep
nsteps = 2

; EM criteria and other stuff emtol = 10
emstep   = 0.01
niter= 20
nbfgscorr = 10

; Output control
nstlog   = 1
nstenergy = 1

; Neighborsearching and short-range nonbonded interactions nstlist= 1
ns_type = grid
pbc   = xyz
rlist   = 1.0

; Electrostatics
coulombtype = PME
rcoulomb  = 1.0

; van der Waals
vdw-type = switch
 rvdw-switch =0.8
rvdw   = 0.9

; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12

; EWALD/PME/PPPM parameters
pme_order = 6
 ewald_rtol  = 1e-06
epsilon_surface  = 0
optimize_fft= no

; Temperature and pressure coupling are off during EM
tcoupl  = no
 pcoupl = no

; Generate velocities to start
gen_vel = no

; options for bonds
constraints = all-bonds

; Type of constraint algorithm
constraint-algorithm = lincs

; Do not constrain the starting configuration
continuation = no

; Highest order in the expansion of the constraint coupling matrix
lincs-order = 12

**

*.itp for tip4p/Ice*

[atomtypes]
;name mass  charge   ptypesigmaepsilon
IW0 0.000   D 0.0   0.0
OW4   15.99940  0.000   A 0.31668   0.88211
HW1.00800   0.000   A 0.0E+00   0.0E+00

[moleculetype]
; name nrexcl
  water  1

[atoms]
; nr type resnr residu atom cgnr charge  mass
1 OW4  1 H2OOW1  1 0 15.994
2 HW   1 H2OHW2  1 0.58971.008
3 HW   1 H2OHW3  1 0.58971.008
4 IW   1 H2OMW4  1-1.17940.0

[constraints]
;i j funct doh  dhh
1   2   1   0.09572
1   3   1   0.09572
2   3   1   0.15139

[exclusions]
1   2   3   4
2   1   3   4
3   1   2   4
4   1   2   3

; The position of the dummy is computed as follows:
;
;   O
;
;   D
;
;   H   H
;
; const = distance (OD) / [ cos (angle(DOH))* distance (OH) ]
; 0.015 nm  / [ cos (52.26 deg) * 0.09572 nm]

; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

[virtual_sites3]
; Dummy fromfunct   a   b
4   1   2   3   1   0.13458 0.13458


*---.itp
for CO2*


[atomtypes]
; namemasscharge ptypesigmaepsilon
   D 22.0049   0.   A  0.   0.
   CA 0.   0.6512   A  0.2757   0.2339
   CO 0.  -0.3256   A  0.3033   0.6695

[moleculetype]
; name  nrexcl
  CO22

[atoms]
; nrtyperesnr   residueatomcgnr   chargemass
  1   D   1  CO2D1   1 0.22.0049
  2   D   1  CO2D2   1 0.22.0049
  3  CA   1  CO2CA   1 0.6512 0.
  4  CO   1  CO2OC1  1-0.3256 0.
  5  CO   1  CO2OC2  1-0.3256 0.

[constraints]
; i   j   functdoc
  1   2 1  0.195948

[virtual_sites2]
; i   j   k   funct   a
  3   1   2 1 0.5
  4   1   2 1 1.08638006
  5   2   1 1 1.08638006



*-*


*.top file*#include "Oplsaa.ff/forcefield.itp"
#include "Oplsaa.ff/atomtype.itp"
#include "Oplsaa.ff/tip4p_Ice.itp"
#include "Oplsaa.ff/co2_epm2_dummy.itp"
[ system ]
; Name
CO2 in water

[ molecules ]
; Compound#mols
  CO2  1
  SOL  460





*-*
Thank you for your time.

Regards,

Sujith



On Tue, May 13, 2014 at 9:57 PM, Justin Lemkul  wrote:

>
>
> On 5/13/14, 11:21 AM, Rasoul Nasiri wrote:
>
>> Why do you think positive values are doubtful?
>> What matters are energy differences b

[gmx-users] why two GTX780ti is slower?

[Albert]

Hello:

I've compiled Gromacs in a GPU machine with two GTX780Ti with following 
command:


env CC=icc F77=ifort CXX=icpc 
CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/intel/impi/4.1.3.049/intel64:/soft/intel/mkl/lib/intel64 
 cmake .. 
-DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF 
-DCMAKE_INSTALL_PREFIX=/soft/gromacs-5.0rc1 -DGMX_MPI=ON -DGMX_GPU=ON 
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda



I've got 40ns/day for a 65,000 atoms membrane system under CHARMM36 FF 
when one GPU is used, but it is only 27ns/day if I used two GPUs. In 
another machine with two GTX690, I used ICC+openmpi instead of ICC+intel 
MPI. The same system, I obtained 40ns/day for one GPU, and 60ns/day for 
two GPU.


I am just wondering, why it is even slower with two GTX780Ti for my 
system, which doesn't happen to GTX690?


thx a lot

Albert
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