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

[Michael Williams]

Hi Szilárd, thank you for the suggestion. I modified the file 
"src/gromacs/gpu_utils/gpu_utils_ocl.cpp” and replaced both instances of 
“#ifdef __APPLE__” with “#if 0”. I then checked that the build and regression 
tests worked without enabling the GPU support. All of the tests passed. Then, 
in a new build folder, I added -DGMX_GPU=ON and -DGMX_USE_OPENCL=ON to the 
Cmake instructions (see below). I did this separately for the unmodified 
version of GROMACS 2018.5 as well as inside a separate copy where I’d made the 
above changes. When I ran “make check” for both the unmodified and modified 
versions, I got the same error as before (logs pasted below). However, it seems 
to happen at different parts of the test suite: the unmodified version passed 
the MdrunTests, then failed on one of the MdrunMpiTests. The modified version 
of GROMACS failed during MdrunTests and then passed the MdrunMpiTests. 

During both runs of the tests I got a system popup asking if I wanted to allow 
the test executable that was running to accept incoming network connections. 
The window was only visible for a few seconds and I didn’t click either option 
(allow / deny) before the window went away again.

Thanks again for your help, and if you have any other ideas I’d be quite 
willing to try them out and let you know the results. 


Mike


Build settings on MacBook Pro (OSX 10.14.3, Mojave) using system clang and 
OpenMP library (from LLVM 7.0.1) built in custom path (no other parts of LLVM 
7.0.1 are installed in this path): 

cmake ..
-DCMAKE_INSTALL_PREFIX=/Users/michael/.local/apps/gromacs-2018.5-apple-clang-omp
 \
-DCMAKE_PREFIX_PATH=/Users/michael/.local \
-DCMAKE_C_COMPILER=/usr/bin/clang \
-DCMAKE_CXX_COMPILER=/usr/bin/clang++ \
-DCMAKE_C_FLAGS="-Wno-deprecated-declarations 
-Wno-unused-command-line-argument -Xpreprocessor -fopenmp -lomp 
-I/Users/michael/.local/include -L/Users/michael/.local/lib” \ 
-DCMAKE_CXX_FLAGS="-Wno-deprecated-declarations 
-Wno-unused-command-line-argument -Xpreprocessor -fopenmp -lomp 
-I/Users/michael/.local/include -L/Users/michael/.local/lib” \ 
-DGMX_FFT_LIBRARY=fftw3 \
-DGMX_GPU=ON \
-DGMX_USE_OPENCL=ON \

-DREGRESSIONTEST_PATH=/Users/michael/.local/source/regressiontests-2018.5

(Note: tabs added to make the above command easier to read)


***ERROR LOG WITH UNMODIFIED GPU_UTILS_OCL.CPP:

Can not increase nstlist because an NVE ensemble is used
Using 2 MPI threads
Using 1 OpenMP thread per tMPI thread

On host veronika.local 1 GPU auto-selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 2 ranks on this node:
  PP:0,PP:0

NOTE: Your choice of number of MPI ranks and amount of resources results in 
using 1 OpenMP threads per rank, which is most likely inefficient. The optimum 
is usually between 2 and 6 threads per rank.
Compilation of source file 
/Users/michael/.local/source/gromacs-2018.5/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-2018.5/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-mpi-test, version 2018.5
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)
MPI rank:1 (out of 2)

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

***ERROR LOG WITH MODIFIED GPU_UTILS_OCL.CPP:

Can not increase nstlist because an NVE ensemble is used
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-2018.5-mod/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 

[gmx-users] Theta and gamma angle between tyrosines

[Archana Sonawani-Jagtap]

Hi,

I have to plot theta and gamma angles between tyrosines throughout the
simulation to check if they are involved in pi-pi interactions. I have
plotted the centroid distance between tyrosines. But don't know which atoms
form theta and gamma angle.

How to get centroid atom for tyrosine using gromacs?

Thanks

Archana
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[gmx-users] Hydrogen bond in z direction

[Mostafa Fakhraee]

Dear all

I want to calculate the number of hydrogen bonds in z direction of
simulation box, in that, the number of hydrogen bonds versus z direction

Would you mind let me know how to do it?

thanks

-- 
 
 Best Regards,
 Mostafa Fakhraee
 ===
 PhD Student of Physical Chemistry,
 Department of Chemistry,
 Sharif University of Technology, Tehran, Iran.
 Official Email: mostafa_fakhr...@ch.sharif.ir 
 Email: mostafa.fakhr...@yahoo.com
  ===
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[gmx-users] gmx select

[Pandya, Akash]

Hi all,

I am running the gmx select command to obtain all my ligand molecules that are 
within a cut-off distance from the COM of a protein residue as a function of 
time. The output from the command below comes with just the atom positions of 
my ligand.


gmx select -f protein_gly.gro -s protein.tpr -n mindist1.ndx -dt 100 -oi 
index.dat -select 'resname LIG and within 3 of res_com of resnr 183' -resnr 
index


Is there a way to only output the residue number instead of the atom numbers?

Akash
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Re: [gmx-users] salvation free energy - gmx bar

[Javier Luque Di Salvo]

Hello Shadfar,

Check your mdp files for missing/repeated init-lambda-state. I had the same
problem, in my case I had two xvg file corresponding to the same
init-lambda-state and in consequence one of them was missing

Cheers
Javier

Date: Thu, 11 Jan 2018 23:33:28 +
> From: "Shadfar, Shamim" 
> To: "gmx-us...@gromacs.org" 
> Subject: [gmx-users] salvation free energy - gmx bar
> Message-ID:
> <
> mexpr01mb02309bf58f609357a035f9dbc3...@mexpr01mb0230.ausprd01.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello everyone,
>
>
> I am doing solvation free energy calculation for a small system
> (Thermodynamic Integration). At the analysis step, gmx bar (gmx bar -f
> md*.xvg -o -oi -oh), I am facing this error, which I never had before. I
> have all my md.xvg files.
>
> Could anyone help me with that?
>
> Here is the error:
>
>
>
> md9.xvg: Ignoring set 'pV (kJ/mol)'.
>
> md9.xvg: 0.0 - 1.0; lambda = (0, 0.9, 0, 0, 0)
>
> dH/dl & foreign lambdas:
>
> dH/dl (mass-lambda) (51 pts)
>
> dH/dl (coul-lambda) (51 pts)
>
> dH/dl (vdw-lambda) (51 pts)
>
> dH/dl (bonded-lambda) (51 pts)
>
> dH/dl (restraint-lambda) (51 pts)
>
> delta H to (0, 0.8, 0, 0, 0) (51 pts)
>
> delta H to (0, 0.9, 0, 0, 0) (51 pts)
>
> delta H to (0, 1, 0, 0, 0) (51 pts)
>
>
> Writing histogram to histogram.xvg
>
>
> Back Off! I just backed up histogram.xvg to ./#histogram.xvg.1#
>
>
> ---
>
> Program: gmx bar, version 2016.3
>
> Source file: src/gromacs/gmxana/gmx_bar.cpp (line 1174)
>
>
> Fatal error:
>
> There is no path between the states X & Y below that is covered by foreign
>
> lambdas:
>
> cannot proceed with BAR.
>
> Use thermodynamic integration of dH/dl by calculating the averages of dH/dl
>
> with g_analyze and integrating them.
>
> Alternatively, use the -extp option if (and only if) the Hamiltonian
>
> depends linearly on lambda, which is NOT normally the case.
>
>
> lambda vector [X]:  init-lambda-state=5 (mass-lambda) l=0 (coul-lambda)
> l=0.5
>
> (vdw-lambda) l=0 (bonded-lambda) l=0 (restraint-lambda) l=0
>
> lambda vector [Y]:  init-lambda-state=7 (mass-lambda) l=0 (coul-lambda)
> l=0.7
>
> (vdw-lambda) l=0 (bonded-lambda) l=0 (restraint-lambda) l=0
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> Shamim Shadfar
>
> PhD Candidate at Massey University
> Institute of Natural and Mathematical Sciences (INMS)
> Centre of Theoretical Chemistry and Physics (CTCP)
>
> Auckland, New Zealand
>
> 
>
>
>
>
> --
>
> --
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> * Please search the archive at
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>
> End of gromacs.org_gmx-users Digest, Vol 165, Issue 41
> **
>
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Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

[Szilárd Páll]

We had some issues with the OS X OpenCL compilers being "special" and not
accepting standard ways of passing include arguments.

Can you try editing the
src/gromacs/gpu_utils/gpu_utils_ocl.cpp
file and replace "#ifdef __APPLE__" with "#if 0", compile the code and see
if that works?

--
Szilárd


On Tue, Feb 19, 2019 at 2:08 AM Michael Williams <
michael.r.c.willi...@gmail.com> wrote:

> 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 <
> 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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Re: [gmx-users] Bond breakage modelling

[Ali Khodayari]

Thank you Peter, I will try to have a detailed look. 
Regards, Ali

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of Peter Kroon
Sent: dinsdag 19 februari 2019 13:41
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Bond breakage modelling

I've never done it myself, so not really. The manual should help :)

I don't know if Morse potentials come built-in, or that you'll need to make
tables.

Be aware that if you have three or more morse potential particles together
they can and will form stable triangles, because there is no influence of
the angle on the potential.


Peter

On 19-02-19 13:35, Ali Khodayari wrote:
> Dear Peter,
>
> Thank you for your prompt reply.
> I think I can try the morse potential to see how the system responds. 
> Could you kindly provide some more info about how to implement it?
> Best regards,
> Ali
>
>
>
>> On 19 Feb 2019, at 11:35, Peter Kroon  wrote:
>>
>> Hi Ali,
>>
>>
>> The short answer is "not really". You could model your bonds as 
>> non-bonded (morse) potentials, but then you lose all angle dependence 
>> on the potential energy, since the non-bonded potentials must be
pair-wise.
>> Depending on the exact problem this may be acceptable though. The 
>> angle dependence on the potential energy also immediately points out 
>> an issue with your cut-off based approach: how will you deal with the
angle(s)?
>>
>> In literature I have seen some papers of people pulling proteins 
>> apart, breaking cystein bridges. Those may contain some insight/ideas.
>>
>>
>> Peter
>>
>>> On 19-02-19 11:28, Ali Khodayari wrote:
>>> Dear All,
>>>
>>>
>>>
>>> We have simulated a cellulose fiber using GLYCAM06 ff parameters 
>>> converted to GROMACS. The model is validated and works properly.
>>>
>>> We are investigating the behavior of the material under tensile load.
>>> However, as covalent bonds are modelled with a harmonic potential 
>>> -as it is in most of the non-reactive force fields- some parameters 
>>> cannot be extracted. Is there any way to mimic the breakage of the 
>>> bonds, let's say when the distance of the atoms exceed a certain 
>>> amount? In other words, if we have a rough idea of the strain at 
>>> which bonds break, can GROMACS neglect bonds from a certain cut-off
onwards?
>>>
>>> Thank you in advanced for your responses.
>>>
>>> Kind regards,
>>>
>>> Ali
>>>
>> --
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>>
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>>
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>>
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send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Bond breakage modelling

[Peter Kroon]

I've never done it myself, so not really. The manual should help :)

I don't know if Morse potentials come built-in, or that you'll need to
make tables.

Be aware that if you have three or more morse potential particles
together they can and will form stable triangles, because there is no
influence of the angle on the potential.


Peter

On 19-02-19 13:35, Ali Khodayari wrote:
> Dear Peter,
>
> Thank you for your prompt reply.
> I think I can try the morse potential to see how the system responds. 
> Could you kindly provide some more info about how to implement it?
> Best regards,
> Ali
>
>
>
>> On 19 Feb 2019, at 11:35, Peter Kroon  wrote:
>>
>> Hi Ali,
>>
>>
>> The short answer is "not really". You could model your bonds as
>> non-bonded (morse) potentials, but then you lose all angle dependence on
>> the potential energy, since the non-bonded potentials must be pair-wise.
>> Depending on the exact problem this may be acceptable though. The angle
>> dependence on the potential energy also immediately points out an issue
>> with your cut-off based approach: how will you deal with the angle(s)?
>>
>> In literature I have seen some papers of people pulling proteins apart,
>> breaking cystein bridges. Those may contain some insight/ideas.
>>
>>
>> Peter
>>
>>> On 19-02-19 11:28, Ali Khodayari wrote:
>>> Dear All,
>>>
>>>
>>>
>>> We have simulated a cellulose fiber using GLYCAM06 ff parameters converted
>>> to GROMACS. The model is validated and works properly.  
>>>
>>> We are investigating the behavior of the material under tensile load.
>>> However, as covalent bonds are modelled with a harmonic potential -as it is
>>> in most of the non-reactive force fields- some parameters cannot be
>>> extracted. Is there any way to mimic the breakage of the bonds, let's say
>>> when the distance of the atoms exceed a certain amount? In other words, if
>>> we have a rough idea of the strain at which bonds break, can GROMACS neglect
>>> bonds from a certain cut-off onwards?
>>>
>>> Thank you in advanced for your responses.
>>>
>>> Kind regards,
>>>
>>> Ali
>>>
>> -- 
>> 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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>> mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Bond breakage modelling

[Ali Khodayari]

Dear Paul,

Thank you for your response. Unfortunately, ReaxFF shows some discrepancies
in some cases when it comes to carbohydrates. Besides, its parameters are
not written for GROMACS. I am looking for maybe a code to mimic this
behavior using the validated force fields for carbohydrates, say GROMOS or
else. 

Kind regards,
Ali

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of Paul Bauer
Sent: dinsdag 19 februari 2019 13:43
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Bond breakage modelling

Hello,

in general I would advise not to use a classical force field to model a
quantum mechanical effect like breaking a bond.
Classical force fields are not parametrized to reproduce those effects, and
while you might get something that looks fine with the morse potential it
would definitely be unphysical.
If you want to study quantum effects, use a QM method for the parts that are
involved in bond breaking, or use a reactive force field like ReaxFF.

Cheers

Paul

On 2019-02-19 13:35, Ali Khodayari wrote:
> Dear Peter,
>
> Thank you for your prompt reply.
> I think I can try the morse potential to see how the system responds.
> Could you kindly provide some more info about how to implement it?
> Best regards,
> Ali
>
>
>
>> On 19 Feb 2019, at 11:35, Peter Kroon  wrote:
>>
>> Hi Ali,
>>
>>
>> The short answer is "not really". You could model your bonds as 
>> non-bonded (morse) potentials, but then you lose all angle dependence 
>> on the potential energy, since the non-bonded potentials must be
pair-wise.
>> Depending on the exact problem this may be acceptable though. The 
>> angle dependence on the potential energy also immediately points out 
>> an issue with your cut-off based approach: how will you deal with the
angle(s)?
>>
>> In literature I have seen some papers of people pulling proteins 
>> apart, breaking cystein bridges. Those may contain some insight/ideas.
>>
>>
>> Peter
>>
>>> On 19-02-19 11:28, Ali Khodayari wrote:
>>> Dear All,
>>>
>>>
>>>
>>> We have simulated a cellulose fiber using GLYCAM06 ff parameters 
>>> converted to GROMACS. The model is validated and works properly.
>>>
>>> We are investigating the behavior of the material under tensile load.
>>> However, as covalent bonds are modelled with a harmonic potential 
>>> -as it is in most of the non-reactive force fields- some parameters 
>>> cannot be extracted. Is there any way to mimic the breakage of the 
>>> bonds, let's say when the distance of the atoms exceed a certain 
>>> amount? In other words, if we have a rough idea of the strain at 
>>> which bonds break, can GROMACS neglect bonds from a certain cut-off
onwards?
>>>
>>> Thank you in advanced for your responses.
>>>
>>> Kind regards,
>>>
>>> Ali
>>>
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Re: [gmx-users] Bond breakage modelling

[Paul Bauer]

Hello,

in general I would advise not to use a classical force field to model a 
quantum mechanical effect like breaking a bond.
Classical force fields are not parametrized to reproduce those effects, 
and while you might get something that looks fine with the morse 
potential it would definitely be unphysical.
If you want to study quantum effects, use a QM method for the parts that 
are involved in bond breaking, or use a reactive force field like ReaxFF.


Cheers

Paul

On 2019-02-19 13:35, Ali Khodayari wrote:

Dear Peter,

Thank you for your prompt reply.
I think I can try the morse potential to see how the system responds.
Could you kindly provide some more info about how to implement it?
Best regards,
Ali




On 19 Feb 2019, at 11:35, Peter Kroon  wrote:

Hi Ali,


The short answer is "not really". You could model your bonds as
non-bonded (morse) potentials, but then you lose all angle dependence on
the potential energy, since the non-bonded potentials must be pair-wise.
Depending on the exact problem this may be acceptable though. The angle
dependence on the potential energy also immediately points out an issue
with your cut-off based approach: how will you deal with the angle(s)?

In literature I have seen some papers of people pulling proteins apart,
breaking cystein bridges. Those may contain some insight/ideas.


Peter


On 19-02-19 11:28, Ali Khodayari wrote:
Dear All,



We have simulated a cellulose fiber using GLYCAM06 ff parameters converted
to GROMACS. The model is validated and works properly.

We are investigating the behavior of the material under tensile load.
However, as covalent bonds are modelled with a harmonic potential -as it is
in most of the non-reactive force fields- some parameters cannot be
extracted. Is there any way to mimic the breakage of the bonds, let's say
when the distance of the atoms exceed a certain amount? In other words, if
we have a rough idea of the strain at which bonds break, can GROMACS neglect
bonds from a certain cut-off onwards?

Thank you in advanced for your responses.

Kind regards,

Ali


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Re: [gmx-users] Bond breakage modelling

[Ali Khodayari]

Dear Peter,

Thank you for your prompt reply.
I think I can try the morse potential to see how the system responds. 
Could you kindly provide some more info about how to implement it?
Best regards,
Ali



> On 19 Feb 2019, at 11:35, Peter Kroon  wrote:
> 
> Hi Ali,
> 
> 
> The short answer is "not really". You could model your bonds as
> non-bonded (morse) potentials, but then you lose all angle dependence on
> the potential energy, since the non-bonded potentials must be pair-wise.
> Depending on the exact problem this may be acceptable though. The angle
> dependence on the potential energy also immediately points out an issue
> with your cut-off based approach: how will you deal with the angle(s)?
> 
> In literature I have seen some papers of people pulling proteins apart,
> breaking cystein bridges. Those may contain some insight/ideas.
> 
> 
> Peter
> 
>> On 19-02-19 11:28, Ali Khodayari wrote:
>> Dear All,
>> 
>> 
>> 
>> We have simulated a cellulose fiber using GLYCAM06 ff parameters converted
>> to GROMACS. The model is validated and works properly.  
>> 
>> We are investigating the behavior of the material under tensile load.
>> However, as covalent bonds are modelled with a harmonic potential -as it is
>> in most of the non-reactive force fields- some parameters cannot be
>> extracted. Is there any way to mimic the breakage of the bonds, let's say
>> when the distance of the atoms exceed a certain amount? In other words, if
>> we have a rough idea of the strain at which bonds break, can GROMACS neglect
>> bonds from a certain cut-off onwards?
>> 
>> Thank you in advanced for your responses.
>> 
>> Kind regards,
>> 
>> Ali
>> 
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Re: [gmx-users] Is there a more efficient way to calculate the "gmx distance" with a very long index?

[ZHANG Cheng]

Can I also ask, I am running it on high performance computer (HPC). So whether 
the cpu (-pe mpi 12) or memory (-l mem=2G) would influence the capability to 
handle a very long index file? 


When the job is submitted, longer queue time will be required if requesting 
more resources. So I want to optimise the cpu and memory with the least queue 
time.


Thank you!


-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Tue, Feb 19, 2019 05:13 AM
To:  "gromacs.org_gmx-users";

Subject:  Is there a more efficient way to calculate the "gmx distance" with a 
very long index?



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] Minimum distance of ligand molecules

[Pandya, Akash]

Hi all,


For example if I have 200 ligand molecules in my system, is there a way of 
plotting the identity of those ligands in the form of an index (e.g. 1,2,3, 
etc...) with minimum distance from the binding sites as function of time?


Akash

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Re: [gmx-users] Bond breakage modelling

[Peter Kroon]

Hi Ali,


The short answer is "not really". You could model your bonds as
non-bonded (morse) potentials, but then you lose all angle dependence on
the potential energy, since the non-bonded potentials must be pair-wise.
Depending on the exact problem this may be acceptable though. The angle
dependence on the potential energy also immediately points out an issue
with your cut-off based approach: how will you deal with the angle(s)?

In literature I have seen some papers of people pulling proteins apart,
breaking cystein bridges. Those may contain some insight/ideas.


Peter

On 19-02-19 11:28, Ali Khodayari wrote:
> Dear All,
>
>  
>
> We have simulated a cellulose fiber using GLYCAM06 ff parameters converted
> to GROMACS. The model is validated and works properly.  
>
> We are investigating the behavior of the material under tensile load.
> However, as covalent bonds are modelled with a harmonic potential -as it is
> in most of the non-reactive force fields- some parameters cannot be
> extracted. Is there any way to mimic the breakage of the bonds, let's say
> when the distance of the atoms exceed a certain amount? In other words, if
> we have a rough idea of the strain at which bonds break, can GROMACS neglect
> bonds from a certain cut-off onwards?
>
> Thank you in advanced for your responses.
>
> Kind regards,
>
> Ali
>
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[gmx-users] Bond breakage modelling

[Ali Khodayari]

Dear All,

 

We have simulated a cellulose fiber using GLYCAM06 ff parameters converted
to GROMACS. The model is validated and works properly.  

We are investigating the behavior of the material under tensile load.
However, as covalent bonds are modelled with a harmonic potential -as it is
in most of the non-reactive force fields- some parameters cannot be
extracted. Is there any way to mimic the breakage of the bonds, let's say
when the distance of the atoms exceed a certain amount? In other words, if
we have a rough idea of the strain at which bonds break, can GROMACS neglect
bonds from a certain cut-off onwards?

Thank you in advanced for your responses.

Kind regards,

Ali

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[gmx-users] analysis following the equlibration of protein-membrane system

[Olga Press]

Dear Gromacs users,
I've performed a membrane-protein simulation by charmm36ff as
described below:
1. 10ns of  NVT equilibration with position restrained on the protein
2. 50ns of NPT equilibration with position restrained on the protein
3. 200ns of  NPT equilibration without position restrained on the protein
Now I would like to calculate analyzes to ensure the stability and the
convergence of the simulation. So, my questions are:

1. Which analysis should I calculate? except for RMSD, the area per lipid,
bilayer-thickness, and temperature, pressure, total-energy, dimensions size
convergence?

2. I divided the equilibration into three parts as described above, should
I concatenate the .edr files from the *whole simulation* to make the
fixed.edr file (meaning from the beginning till the end (from NVT to
NPT_without restrains) in order to create the xvg files?

3. Following the equilibration of the whole system, I would like to run the
simulation itself. I'm working on a dimer (amyloid)-membrane system and I'm
interested in the interactions between the two attached monomers and the
membrane. Now my question is should I release the H-bond constraints in the
production step? and if so, what should I put at the constraints category
at the mdp file?  in this step I will not use the position restrains but
what about the H-bond constraints?

Thanks in advance
Olga
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