Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

2019-02-18 Thread Schulz, Roland 
Hi,

Intel GPUs require cluster size 4. AMD GPUs perform best with 8.
Does GROMACS recognize both GPUs (should be in the log file) if you compile 
with cluster size 4? If so you should be able to select which GPU it uses with 
the -gpuid command line argument. But I have never tried it with multiple 
vendors so I'm not sure it actually works.

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> Michael Williams
> Sent: Monday, February 18, 2019 6:32 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro
> with AMD Radeon Pro 560 GPU
> 
> Hi Roland,
> 
> Thank you for the reply. The file (nbnxn_ocl_kernel_pruneonly.clh) does
> exist in that folder, so I’m not sure why it isn’t being located. I’ve
> downloaded the latest versions of Gromacs, and I will try building them as
> soon as I can.
> 
> Is there any reason to specify -DGMX_OCL_NB_CLUSTER_SIZE=4 as
> mentioned in the install manual for Intel GPUs? Based on the output below,
> Gromacs seems to recognize the AMD GPU, although the laptop does also
> have an integrated Intel graphics chip. Thanks again,
> 
> 
> Mike
> 
> > On Feb 19, 2019, at 1:13 PM, Schulz, Roland 
> wrote:
> >
> > Hi,
> >
> > Does the nbnxn_ocl_kernel_pruneonly.clh file exist in the
> /Users/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl
> folder?
> > When reporting errors you should always check with the latest version. The
> latest versions are 2019.1 and 2018.5.
> >
> > Roland
> >
> >> -Original Message-
> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf
> >> Of Michael Williams
> >> Sent: Monday, February 18, 2019 5:08 PM
> >> To: gromacs.org_gmx-users 
> >> Subject: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro
> with
> >> AMD Radeon Pro 560 GPU
> >>
> >> Hi, I’ve been trying to build Gromacs 2018.3 on my MacBook Pro (in
> >> OSX 10.14.3). I saw online (https://redmine.gromacs.org/issues/2369
> >> ) that Gromacs with GPU
> >> support via OpenCL was found to work a similar computer, but I have
> >> not had any luck. Is there a way to see what settings (compiler,
> >> CMake variables, etc) were used for that build? Or if anyone has any
> >> suggestions, I’d be very grateful. Thanks for your help,
> >>
> >> Mike
> >>
> >> The errors that I have been getting while running “make check” look like:
> >>
> >>
> >> 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/michael/.local/source/gromacs-
> >> 2018.3/src/gromacs/mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl failed!
> >> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_ -
> >> DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -
> DLJ_COMB_GEOM
> >> -DVDWNAME=_VdwLJCombGeom -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 -cl- denorms-are-zero
> >> -I/Users/michael/.local/source/gromacs-
> >> 2018.3/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"
> >> ^
> >> ---LOG END
> >>
> >> ---
> >> Program: mdrun-test, version 2018.3
> >> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 507)
> >> 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
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
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> >> send a mail to gmx-users-requ...@gromacs.org.
> > --
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Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

2019-02-18 Thread Michael Williams 
Hi Roland,

Thank you for the reply. The file (nbnxn_ocl_kernel_pruneonly.clh) does exist 
in that folder, so I’m not sure why it isn’t being located. I’ve downloaded the 
latest versions of Gromacs, and I will try building them as soon as I can. 

Is there any reason to specify -DGMX_OCL_NB_CLUSTER_SIZE=4 as mentioned in the 
install manual for Intel GPUs? Based on the output below, Gromacs seems to 
recognize the AMD GPU, although the laptop does also have an integrated Intel 
graphics chip. Thanks again,


Mike

> On Feb 19, 2019, at 1:13 PM, Schulz, Roland  wrote:
> 
> Hi,
> 
> Does the nbnxn_ocl_kernel_pruneonly.clh file exist in the 
> /Users/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl 
> folder?
> When reporting errors you should always check with the latest version. The 
> latest versions are 2019.1 and 2018.5.
> 
> Roland
> 
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
>> Michael Williams
>> Sent: Monday, February 18, 2019 5:08 PM
>> To: gromacs.org_gmx-users 
>> Subject: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with
>> AMD Radeon Pro 560 GPU
>> 
>> Hi, I’ve been trying to build Gromacs 2018.3 on my MacBook Pro (in OSX
>> 10.14.3). I saw online (https://redmine.gromacs.org/issues/2369
>> ) that Gromacs with GPU
>> support via OpenCL was found to work a similar computer, but I have not had
>> any luck. Is there a way to see what settings (compiler, CMake variables, 
>> etc)
>> were used for that build? Or if anyone has any suggestions, I’d be very
>> grateful. Thanks for your help,
>> 
>> Mike
>> 
>> The errors that I have been getting while running “make check” look like:
>> 
>> 
>> 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/michael/.local/source/gromacs-
>> 2018.3/src/gromacs/mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl failed!
>> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_ -
>> DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -
>> DLJ_COMB_GEOM -DVDWNAME=_VdwLJCombGeom -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 -cl-
>> denorms-are-zero -I/Users/michael/.local/source/gromacs-
>> 2018.3/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"
>> ^
>> ---LOG END
>> 
>> ---
>> Program: mdrun-test, version 2018.3
>> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 507)
>> 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
>> --
>> 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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>> a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

2019-02-18 Thread Schulz, Roland 
Hi,

Does the nbnxn_ocl_kernel_pruneonly.clh file exist in the 
/Users/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl folder?
When reporting errors you should always check with the latest version. The 
latest versions are 2019.1 and 2018.5.

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> Michael Williams
> Sent: Monday, February 18, 2019 5:08 PM
> To: gromacs.org_gmx-users 
> Subject: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with
> AMD Radeon Pro 560 GPU
> 
> Hi, I’ve been trying to build Gromacs 2018.3 on my MacBook Pro (in OSX
> 10.14.3). I saw online (https://redmine.gromacs.org/issues/2369
> ) that Gromacs with GPU
> support via OpenCL was found to work a similar computer, but I have not had
> any luck. Is there a way to see what settings (compiler, CMake variables, etc)
> were used for that build? Or if anyone has any suggestions, I’d be very
> grateful. Thanks for your help,
> 
> Mike
> 
> The errors that I have been getting while running “make check” look like:
> 
> 
> 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/michael/.local/source/gromacs-
> 2018.3/src/gromacs/mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl failed!
> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_ -
> DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -
> DLJ_COMB_GEOM -DVDWNAME=_VdwLJCombGeom -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 -cl-
> denorms-are-zero -I/Users/michael/.local/source/gromacs-
> 2018.3/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"
>  ^
> ---LOG END
> 
> ---
> Program: mdrun-test, version 2018.3
> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 507)
> 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
> --
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[gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

2019-02-18 Thread Michael Williams 
Hi, I’ve been trying to build Gromacs 2018.3 on my MacBook Pro (in OSX 
10.14.3). I saw online (https://redmine.gromacs.org/issues/2369 
) that Gromacs with GPU support via 
OpenCL was found to work a similar computer, but I have not had any luck. Is 
there a way to see what settings (compiler, CMake variables, etc) were used for 
that build? Or if anyone has any suggestions, I’d be very grateful. Thanks for 
your help,

Mike

The errors that I have been getting while running “make check” look like:


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/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl
 failed!
-- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_ -DGMX_OCL_FASTGEN 
-DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM -DVDWNAME=_VdwLJCombGeom 
-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 
-cl-denorms-are-zero 
-I/Users/michael/.local/source/gromacs-2018.3/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"
 ^
---LOG END

---
Program: mdrun-test, version 2018.3
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 507)
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
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[gmx-users] Is there a more efficient way to calculate the "gmx distance" with a very long index?

2019-02-18 Thread ZHANG Cheng 
My coarse-grained system has 10 proteins, each has 442 residues. After a period 
of time, those proteins aggregated. I want to use "gmx distance" to know which 
residues most likely to involve contact with other proteins.


I prepared a index.ndx file, in which there are 442*442*(9+8+7 ... + 1) = 
8791380 pairs of atom indices. But these indices are extremely too long for 
Gromacs to handle at a time. So I have to split it into shorter pieces.


But is there a more efficient way to achieve this?


Thank you!


Cheng
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[gmx-users] How to replacing molecule outside the 2.5nm cutoff distance from protein surface in gromacs?

2019-02-18 Thread Shweta Kumari 
Dear gromacs users,
I have protein-membrane (POPC only) system. I want to replace the
cholesterol molecules with POPC but outside a 2.5nm cutoff distance of
protein surface.
I am using this command :
gmx insert-molecules -f system.gro -ci cholesterol.pdb -nmol 10 -try 10
-replace POPC -o output.pdb
But this command randomly select the POPC molecules and replace it with
cholesterol. In this way few cholesterol molecules are coming near the
protein (within 2nm).
Thanks in advance!

Best Regards,
Shweta
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[gmx-users] Making Polyamide membrane itp file

2019-02-18 Thread 이영규 
Dear gromacs users,

These days, I am working on Polyamide membrane osmosis. And I am struggling
with making a topology file. I've read a paper " *DOI: *
10.1021/acs.jpcb.6b06560 " . The author provides pdb file for the
constructed membrane in supporting information section on the webpage. But
to do simulation, it is necessary to make "itp file. However, I don't know
how to make the file. I read the instruction in "
http://www.gromacs.org/Documentation/How-tos/Polymers;, but still I am
lost. Please give me a hand!!

Thanks in advance!

Sincerely

-- 

Yeongkyu Lee

M.S student

Department of Physics

501, Jinjudaero, Jinju, Gyeongnam
,
52828, Korea

Email: monsterpl...@gmail.com

Phone: +82-10-8771-2190
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[gmx-users] Computational performance in version 2019-beta3.

2019-02-18 Thread Edjan Silva 
Hello guys,

I performed a 100 ns simulation using GROMACS: gmx mdrun, version
2019-beta3. The performance of my computer was 4ns / day. In previous
versions, I performed similar simulations and obtained performace of 40 ns
/ day.

I would like to know if something has changed in gmx mdrun's input (version
2019-beta3), for better performance.

Simulation details:

B-DNA and small ligand.
solvent and added ions
Octahedral box 1.0 nm
simulation time: 100 ns - nsteps = 5000 - dt = 0.02

Computer Details:

Memory: 31.3 GiB
Processor: intel Xeon (R) CPU E5-1650 v3 @ 3.50GHz x 12
Graphics: NVF1
Disk: 1 TB free

Kind regards,

Edjan.
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[gmx-users] Building Gromacs on a MacBook Pro with AMD Radeon Pro 560

2019-02-18 Thread Michael Williams 
Hello, I’ve been having trouble building Gromacs 2018.3 on my MacBook Pro. I 
would like to be able to use OpenMP as well as the GPU (via OpenCL). I’ve 
searched for successful builds with similar systems described on this email 
list, but haven’t found anything that worked yet. 

Based on what I’ve read on this email list and various searches elsewhere, I am 
trying to build Gromacs 2018.3 using the OS X (10.14.3, Mojave) system default 
clang compiler (so that there is no compiler mismatch with the system OpenCL 
libraries). Since it does not have OpenMP support by default, I compiled libomp 
using the system’s clang. (As a side note, I built static libomp libraries). 

I installed the custom libomp with a prefix of $HOME/.local , which is mostly 
empty except for Cmake. When I built Gromacs, I used the following command: 

cmake .. -DGMX_BUILD_OWN_FFTW=ON \
-DCMAKE_INSTALL_PREFIX=/Users/michael/.local/apps/gromacs-2018.3-apple-clang-omp-ocl
 \
-DCMAKE_PREFIX_PATH=/Users/michael/.local \
-DREGRESSIONTEST_PATH=/Users/michael/.local/source/regressiontests-2018.3 \
-DCMAKE_C_FLAGS="-Xpreprocessor -fopenmp -lomp -I/Users/michael/.local/include 
-L/Users/michael/.local/lib” \
-DCMAKE_CXX_FLAGS="-Xpreprocessor -fopenmp -lomp 
-I/Users/michael/.local/include -L/Users/michael/.local/lib” \
-DGMX_GPU=ON \
-DGMX_USE_OPENCL=ON

Next I ran "make -j 4" and I didn’t get any errors during building (although I 
got the following warnings many times: clang: warning: -lomp: 'linker' input 
unused [-Wunused-command-line-argument]
clang: warning: argument unused during compilation: 
'-L/Users/michael/.local/lib' [-Wunused-command-line-argument]). 

However, when I ran "make check”, I got the errors pasted below. For the 
record, when I compiled the same version of Gromacs with the same configuration 
settings as above except with no GPU support, all of the tests passed. 

Any help or suggestions would be very much appreciated. Thanks kindly!

Mike


Errors during tests:

….
Using 1 MPI thread
Using 1 OpenMP 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/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl
 failed!
-- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_ -DGMX_OCL_FASTGEN 
-DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM -DVDWNAME=_VdwLJCombGeom 
-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 
-cl-denorms-are-zero 
-I/Users/michael/.local/source/gromacs-2018.3/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"
 ^
---LOG END

---
Program: mdrun-test, version 2018.3
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 507)
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

Followed by:

Abnormal return value for ' gmx mdrun -ntmpi 12  -notunepme >mdrun.out 
2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 12-ntomp 1  -notunepme 
>mdrun.out 2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 12-ntomp 1  -notunepme 
>mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
FAILED. Check mdrun.out, md.log file(s) in dd121 for dd121

Abnormal return value for ' gmx mdrun   -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in nbnxn_pme_order5 for nbnxn_pme_order5

Abnormal return value for ' gmx mdrun   -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in nbnxn_rzero for nbnxn_rzero

Abnormal return value for ' gmx mdrun -ntmpi 6  -notunepme >mdrun.out 2>&1' 
was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 6-ntomp 1  -notunepme 
>mdrun.out 2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 1  -notunepme >mdrun.out 2>&1' 
was -1
FAILED. Check mdrun.out, md.log file(s) in orientation-restraints for 
orientation-restraints

Abnormal return value for ' gmx mdrun   -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in position-restraints for 
position-restraints

Abnormal return value for ' gmx mdrun   -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in pull_geometry_angle for 
pull_geometry_angle

Abnormal return value for ' gmx

Re: [gmx-users] Error while running grompp command

2019-02-18 Thread Bratin Kumar Das 
Please send the entire error message

On Sun 17 Feb, 2019, 8:16 PM Nath, Dinesh  Hello,
>
> I am running the gmx grompp -f ions.mdp -c solv.gro -p topol.top -o
> ions.tpr
>
> And this is the error I am getting:
>
> ERROR 1 [file rew.prm, line 36]:
>   Encountered a second block of parameters for dihedral type 9 for the same
>   atoms, with either different parameters and/or the first block has
>   multiple lines. This is not supported.
>
> Any advice to fix it.
>
> Thank you in advance.
>
>
> __
> Dinesh Nath, Ph.D.
> The University of Oklahoma
> Postdoctoral Research Fellow
> Department of Chemistry & Biochemistry
> Institute for Natural Products Applications
> & Research Technologies (INPART)
> 101 Stephenson Parkway
> Norman, OK 73019
> (412) 908-3476
> dinesh.nat...@ou.edu
>
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