[gmx-users] Magic Number Error in XTC file (read 0, should be 1995)

[Naga Sundar]

Dear users

Its a 50 ns protein-ligand simulation, i have been
generated multiple xtc files. Now trying to concordinate as single.xtc
file. But unfortunately the process under trouble and its showing the error

Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)

I have no idea about this problem, plz help me to troubleshoot the error.

-- 
Regards
N.Nagasundaram
DST N-PDF
Centre for Nanoscience and Nanotechnology
Sathyabama University
Chennai, India
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Re: [gmx-users] liquid-solid/liquid-air interface simulations

[André Farias de Moura]

Hi Junjun,

It is possible to cut a rhomboid shape out of hexagonal lattice (I did that
recently to build a graphite substrate). As a matter of fact, it works for
other lattice shapes as well (we've being doing that lately for things as
different as titania, hematite and even a CoO spinel). you just need to
care about the box lengths in each direction, to make sure that periodic
images are located at the correct distance to preserve bond lengths and
angles across the boundaries. I usually use VMD, but there are other
software you might consider (Vesta, Jmol, Avogadro, etc). Depending on the
software you choose, you'll have to dig a little bit in the documentation
to grab the commands ans scripts that need to be used in each case.

periodic boundaries conditions need to be applied in all three directions,
so you have to increase the box length in one of the directions to create a
vacuum region large enough to avoid any interaction between mirror images
of the system in that direction (compressibility needs to be set to zero in
that direction in order to avoid the box being scaled down to suppress the
vacuum region).

You might want to take a look a these papers:

Phys. Chem. Chem. Phys., 2015,17, 3820-3831
Langmuir, 2015, 31 (40), pp 10995–11004
J. Phys. Chem. B, 2005, 109 (9), pp 4032–4041

I hope it helps.

Andre

On Thu, May 26, 2016 at 12:03 PM, liu junjun  wrote:

> Hello
>
> I am new to Gromacs and hope to get some suggestions on liquid-solid
> interface as well as liquid-air interface simulations.
>
> I have two questions:
> 1. how to set up a solid interface from hexaghal crystal unit cell? I
> assume the simulation system need solid to be in a cubic shape so that the
> periodic condition could be applied. But how to convert the hexaghal shape
> to cublic shape for the solid?
> 2. Is it possible to apply the 2D periodic boundary condition? For
> liquid-air interface, the periodic boundary condition should not be applied
> on Z-axes as the gas-phase will be considered just as vacuum.
>
> It's highly appreciated if there are any suggestions, literature,
> tutorials.
>
>
> Junjun
> --
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-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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[gmx-users] Lipid Head group Orientation

[Nidhin Thomas]

Hi GROMACS Users,

This question was asked before in the forum. But I could not find a complete 
answer. So I’m asking again. Is there any command in GROMACS that can give the 
orientation of lipid head groups of all lipids averaged over time?

I wrote a code which takes the co-ordinates of P and N atoms at each time 
frames and gives the orientation of P-N vector averaged over the time. I was 
wondering if there is any command in GROMACS that can provide this data 
directly ?

I used g_sgangle command to obtain the angles of one lipid molecule. But how do 
we get the data for all lipids in one file?

Thanks,
Nidhin Thomas
University of Houston
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Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

[Mark Abraham]

Hi,

Is clang 3.8 supported by CUDA on Mac?

Mark

On Thu, 26 May 2016 21:05 Uliano Guerrini  wrote:

> here is part of the log:
>
> GROMACS version:VERSION 5.1.2
> Precision:  single
> Memory model:   64 bit
> MPI library:thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support:enabled
> OpenCL support: disabled
> invsqrt routine:gmx_software_invsqrt(x)
> SIMD instructions:  SSE4.1
> FFT library:fftw-3.3.4-sse2-avx
> RDTSCP usage:   enabled
> C++11 compilation:  disabled
> TNG support:enabled
> Tracing support:disabled
> Built on:   Gio 26 Mag 2016 20:29:04 CEST
> Built by:   uli...@macpro.lan [CMAKE]
> Build OS/arch:  Darwin 15.5.0 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:Intel(R) Xeon(R) CPU   W3680  @ 3.33GHz
> Build CPU family:   6   Model: 44   Stepping: 2
> Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
> sse4.2 ssse3
> C compiler: /opt/local/bin/clang Clang 3.8.0
> C compiler flags:-msse4.1-Wall -Wno-unused -Wunused-value
> -Wunused-parameter  -O3 -DNDEBUG
> C++ compiler:   /opt/local/bin/clang++ Clang 3.8.0
> C++ compiler flags:  -msse4.1-Wextra -Wno-missing-field-initializers
> -Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG
> Boost version:  1.55.0 (internal)
> CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda
> compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on
> Mon_Apr_11_13:23:40_CDT_2016;Cuda compilation tools, release 7.5, V7.5.26
> CUDA compiler
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;
> ;-msse4.1;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;
> CUDA driver:0.0
> CUDA runtime:   0.0
>
>
> NOTE: Error occurred during GPU detection:
>   CUDA driver version is insufficient for CUDA runtime version
>   Can not use GPU acceleration, will fall back to CPU kernels.
>
> regarding osx equivalent of ldd I found otool -L
>
> uliano@MacPro:/opt/gromacs/bin$ otool -L gmx
> gmx:
> @rpath/libgromacs.1.dylib (compatibility version 1.0.0, current
> version 1.2.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 1226.10.1)
> /opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current
> version 1.2.8)
> /opt/local/lib/libfftw3f.3.dylib (compatibility version 8.0.0,
> current version 8.4.0)
>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
> (compatibility version 1.0.0, current version 4.0.0)
> /opt/local/lib/libomp/libomp.dylib (compatibility version 5.0.0,
> current version 5.0.0)
> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current
> version 120.1.0)
>
> and
>
> uliano@MacPro:/opt/gromacs/lib$ otool -L libgromacs.1.dylib
> libgromacs.1.dylib:
> @rpath/libgromacs.1.dylib (compatibility version 1.0.0, current
> version 1.2.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 1226.10.1)
> /opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current
> version 1.2.8)
> /opt/local/lib/libfftw3f.3.dylib (compatibility version 8.0.0,
> current version 8.4.0)
>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
> (compatibility version 1.0.0, current version 4.0.0)
> /opt/local/lib/libomp/libomp.dylib (compatibility version 5.0.0,
> current version 5.0.0)
> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current
> version 120.1.0)
>
> no sign of cuda here, however cmake did find it
>
> ...
> -- Found CUDA: /usr/local/cuda (found suitable version "7.5", minimum
> required is "4.0”)
> …
>
> and the build process didn’t gave any error
>
> here is a report of export DYLD_PRINT_LIBRARIES=TRUE that prints libraries
> as they are loaded
>
> uliano@MacPro:~/demo$ /opt/gromacs/bin/gmx mdrun -v -deffnm md_0_1
> dyld: loaded: /opt/gromacs/bin/gmx
> dyld: loaded: /opt/gromacs/bin/../lib/libgromacs.1.dylib
> dyld: loaded: /usr/lib/libSystem.B.dylib
> dyld: loaded: /opt/local/lib/libz.1.dylib
> dyld: loaded: /opt/local/lib/libfftw3f.3.dylib
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
> dyld: loaded: /opt/local/lib/libomp/libomp.dylib
> dyld: loaded: /usr/lib/libc++.1.dylib
> dyld: loaded: /usr/lib/system/libcache.dylib
> dyld: loaded: /usr/lib/system/libcommonCrypto.dylib
> dyld: loaded: /usr/lib/system/libcompiler_rt.dylib
> dyld: loaded: /usr/lib/system/libcopyfile.dylib
> dyld: loaded: /usr/lib/system/libcorecrypto.dylib
> 

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

[Uliano Guerrini]

here is part of the log:

GROMACS version:VERSION 5.1.2
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:enabled
OpenCL support: disabled
invsqrt routine:gmx_software_invsqrt(x)
SIMD instructions:  SSE4.1
FFT library:fftw-3.3.4-sse2-avx
RDTSCP usage:   enabled
C++11 compilation:  disabled
TNG support:enabled
Tracing support:disabled
Built on:   Gio 26 Mag 2016 20:29:04 CEST
Built by:   uli...@macpro.lan [CMAKE]
Build OS/arch:  Darwin 15.5.0 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU   W3680  @ 3.33GHz
Build CPU family:   6   Model: 44   Stepping: 2
Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr 
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 
sse4.2 ssse3
C compiler: /opt/local/bin/clang Clang 3.8.0
C compiler flags:-msse4.1-Wall -Wno-unused -Wunused-value 
-Wunused-parameter  -O3 -DNDEBUG  
C++ compiler:   /opt/local/bin/clang++ Clang 3.8.0
C++ compiler flags:  -msse4.1-Wextra -Wno-missing-field-initializers 
-Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG  
Boost version:  1.55.0 (internal)
CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler 
driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on 
Mon_Apr_11_13:23:40_CDT_2016;Cuda compilation tools, release 7.5, V7.5.26
CUDA compiler 
flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;
 
;-msse4.1;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;
CUDA driver:0.0
CUDA runtime:   0.0


NOTE: Error occurred during GPU detection:
  CUDA driver version is insufficient for CUDA runtime version
  Can not use GPU acceleration, will fall back to CPU kernels.

regarding osx equivalent of ldd I found otool -L

uliano@MacPro:/opt/gromacs/bin$ otool -L gmx
gmx:
@rpath/libgromacs.1.dylib (compatibility version 1.0.0, current version 
1.2.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 1226.10.1)
/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current 
version 1.2.8)
/opt/local/lib/libfftw3f.3.dylib (compatibility version 8.0.0, current 
version 8.4.0)
/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate 
(compatibility version 1.0.0, current version 4.0.0)
/opt/local/lib/libomp/libomp.dylib (compatibility version 5.0.0, 
current version 5.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
120.1.0)

and 

uliano@MacPro:/opt/gromacs/lib$ otool -L libgromacs.1.dylib 
libgromacs.1.dylib:
@rpath/libgromacs.1.dylib (compatibility version 1.0.0, current version 
1.2.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 1226.10.1)
/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current 
version 1.2.8)
/opt/local/lib/libfftw3f.3.dylib (compatibility version 8.0.0, current 
version 8.4.0)
/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate 
(compatibility version 1.0.0, current version 4.0.0)
/opt/local/lib/libomp/libomp.dylib (compatibility version 5.0.0, 
current version 5.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
120.1.0)

no sign of cuda here, however cmake did find it 

...
-- Found CUDA: /usr/local/cuda (found suitable version "7.5", minimum required 
is "4.0”) 
…

and the build process didn’t gave any error

here is a report of export DYLD_PRINT_LIBRARIES=TRUE that prints libraries as 
they are loaded

uliano@MacPro:~/demo$ /opt/gromacs/bin/gmx mdrun -v -deffnm md_0_1 
dyld: loaded: /opt/gromacs/bin/gmx
dyld: loaded: /opt/gromacs/bin/../lib/libgromacs.1.dylib
dyld: loaded: /usr/lib/libSystem.B.dylib
dyld: loaded: /opt/local/lib/libz.1.dylib
dyld: loaded: /opt/local/lib/libfftw3f.3.dylib
dyld: loaded: 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
dyld: loaded: /opt/local/lib/libomp/libomp.dylib
dyld: loaded: /usr/lib/libc++.1.dylib
dyld: loaded: /usr/lib/system/libcache.dylib
dyld: loaded: /usr/lib/system/libcommonCrypto.dylib
dyld: loaded: /usr/lib/system/libcompiler_rt.dylib
dyld: loaded: /usr/lib/system/libcopyfile.dylib
dyld: loaded: /usr/lib/system/libcorecrypto.dylib
dyld: loaded: /usr/lib/system/libdispatch.dylib
dyld: loaded: /usr/lib/system/libdyld.dylib
dyld: loaded: /usr/lib/system/libkeymgr.dylib
dyld: loaded: /usr/lib/system/liblaunch.dylib
dyld: loaded: /usr/lib/system/libmacho.dylib
dyld: loaded: /usr/lib/system/libquarantine.dylib
dyld: loaded: 

[gmx-users] Relaxation Test

[khourshaeishargh]

Dear GROMACS user
During the last 3 weeks, I confront with a really though problem  through
my M.Sc thesis. I don't now if you are familiar with Relaxation test in
Mechanical Engineering or not, simply It is a test In which we exert a
constant strain to a simulation box and monitor its Stress changes versus
time. so my question is: how can I exert constant strain to a simulation
box ?! from bottom of my heart I implore you not to say : use NEMD option.
If I should use NEMD in .mdp file option, please give me the explicit
changes in my .mdp file. suppose that I want to give a stepwise strain
with amplitude of 5 percentage through X-direction.
I really appreciate it, If anyone could help me please, also If it's not
possible please tell me.

best  regards, Ali

==

Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)

Department of Mechanical Engineering

Sharif University of Technology, Tehran, Iran
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Re: [gmx-users] free energy calculation on amino acid mutation

[Mark Abraham]

Hi,

I understand pmx is built exactly for this task.

Mark

On Thu, 26 May 2016 19:35  wrote:

> That really depends on how you approach the problem.
>
> When you choose a dual topology approach you would need to decide where to
> branch off but basically end up with duplicating parts of the residue.
> Sounds like that's what you were trying to do.
>
> In the single topology approach you would match as many atoms as possible
> and balance just the missing atoms with dummies (as opposed to the dual
> approach where you may have lots of them).  As the bonded network stays the
> same you would not need to make any modifications to those.  I do not see
> any reason why you would not want to use this approach in your specific
> case (LEU->GLY).
>
> There is a tool out there that you should probably give a try: pmx.  I
> believe it uses the single topology approach.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Yi An [
> anyiphys...@gmail.com]
> Sent: 26 May 2016 17:44
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] free energy calculation on amino acid mutation
>
> Hi Gromacs users,
>
> I'm trying to calculate the relative binding free energy of a certain
> ligand when a leucine in the ligand binding site is mutated to glycine. The
> concept is simple but I have met some difficulties creating topology files
> for free energy calculation. I have two questions I wish you guys can help:
>
> 1. Let's say my protein have 200 residues and the leucine I want to mutate
> is in the middle (80 for example). When I tried to edit the topology of
> this protein, I found that since the number of atoms changed, I need to
> make lots of changes for bond, angle, and dihedral parameters. Is my
> feeling correct?
>
> 2. If my understanding is correct, I wish there are some existing scripts
> which can help people create topology file for mutational free energy
> calculation. I will highly appreciate if you guys tell me where I can find
> them.
>
> Thank you very much.
>
>
> Yi An
> Postdoctoral Research Associate
> UNC-Chapel Hill
> --
> 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] free energy calculation on amino acid mutation

[hannes.loeffler]

That really depends on how you approach the problem.

When you choose a dual topology approach you would need to decide where to 
branch off but basically end up with duplicating parts of the residue.  Sounds 
like that's what you were trying to do.

In the single topology approach you would match as many atoms as possible and 
balance just the missing atoms with dummies (as opposed to the dual approach 
where you may have lots of them).  As the bonded network stays the same you 
would not need to make any modifications to those.  I do not see any reason why 
you would not want to use this approach in your specific case (LEU->GLY).

There is a tool out there that you should probably give a try: pmx.  I believe 
it uses the single topology approach.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Yi An 
[anyiphys...@gmail.com]
Sent: 26 May 2016 17:44
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] free energy calculation on amino acid mutation

Hi Gromacs users,

I'm trying to calculate the relative binding free energy of a certain
ligand when a leucine in the ligand binding site is mutated to glycine. The
concept is simple but I have met some difficulties creating topology files
for free energy calculation. I have two questions I wish you guys can help:

1. Let's say my protein have 200 residues and the leucine I want to mutate
is in the middle (80 for example). When I tried to edit the topology of
this protein, I found that since the number of atoms changed, I need to
make lots of changes for bond, angle, and dihedral parameters. Is my
feeling correct?

2. If my understanding is correct, I wish there are some existing scripts
which can help people create topology file for mutational free energy
calculation. I will highly appreciate if you guys tell me where I can find
them.

Thank you very much.


Yi An
Postdoctoral Research Associate
UNC-Chapel Hill
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[gmx-users] free energy calculation on amino acid mutation

[Yi An]

Hi Gromacs users,

I'm trying to calculate the relative binding free energy of a certain
ligand when a leucine in the ligand binding site is mutated to glycine. The
concept is simple but I have met some difficulties creating topology files
for free energy calculation. I have two questions I wish you guys can help:

1. Let's say my protein have 200 residues and the leucine I want to mutate
is in the middle (80 for example). When I tried to edit the topology of
this protein, I found that since the number of atoms changed, I need to
make lots of changes for bond, angle, and dihedral parameters. Is my
feeling correct?

2. If my understanding is correct, I wish there are some existing scripts
which can help people create topology file for mutational free energy
calculation. I will highly appreciate if you guys tell me where I can find
them.

Thank you very much.


Yi An
Postdoctoral Research Associate
UNC-Chapel Hill
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[gmx-users] free energy calculation on amino acid mutation

[Yi An]

Hi Gromacs users,

I'm trying to calculate the relative binding free energy of a certain
ligand when a leucine in the ligand binding site is mutated to glycine. The
concept is simple but I have met some difficulties creating topology files
for free energy calculation. I have two questions I wish you guys can help:

1. Let's say my protein have 200 residues and the leucine I want to mutate
is in the middle (80 for example). When I tried to edit the topology of
this protein, I found that since the number of atoms changed, I need to
make lots of changes for bond, angle, and dihedral parameters. Is my
feeling correct?

2. If my understanding is correct, I wish there are some existing scripts
which can help people create topology file for mutational free energy
calculation. I will highly appreciate if you guys tell me where I can find
them.

Thank you very much.

Yi An
Postdoctoral Research Associate
UNC-Chapel Hill
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[gmx-users] liquid-solid/liquid-air interface simulations

[liu junjun]

Hello

I am new to Gromacs and hope to get some suggestions on liquid-solid
interface as well as liquid-air interface simulations.

I have two questions:
1. how to set up a solid interface from hexaghal crystal unit cell? I
assume the simulation system need solid to be in a cubic shape so that the
periodic condition could be applied. But how to convert the hexaghal shape
to cublic shape for the solid?
2. Is it possible to apply the 2D periodic boundary condition? For
liquid-air interface, the periodic boundary condition should not be applied
on Z-axes as the gas-phase will be considered just as vacuum.

It's highly appreciated if there are any suggestions, literature, tutorials.


Junjun
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Re: [gmx-users] Ion flux through membrane protein

[Maximilien LOPES RODRIGUES]

 Hello Carsten, thank you very much for your answer.

I read the GROMACS manual and your papers. The new method you developed seems 
very interesting and accurate but it appears much more complicated than 
expected. I don't know if I will be able to properly run a such simulation. I 
still have so much to learn

Basically, these are the main questions I want to answer by simulation:
- Is my protein more permeable to anion or cation ?
- Is it more selective for K+ or Na+ (for instance) ?
- Does this solute pass through the channel and how ?

I am not sure if calculating an exact flux is very relevant now. I should have 
wrote a more accurate title for my first question, sorry !

There are numerous papers about ions transport through membrane protein but 
they don't explain how to reproduce (step by step) such simulation.

Thank you again.
Kind regards,
Max
 
 
Le Jeudi 26 Mai 2016 11:58 CEST, 
gromacs.org_gmx-users-requ...@maillist.sys.kth.se a écrit: 

> Hi Maximilien,
> 
> depending on what exactly the questions are that you like to address, the 
> double-membrane
> setup as used in computational electrophysiology setups might be helpful for 
> you.
> There is a section in the GROMACS PDF manual about that, and there are these 
> two papers:
> http://www.sciencedirect.com/science/article/pii/S0005273616300360
> http://www.mpibpc.mpg.de/275657/Kutzner_2011_BPJ_101_809-817.pdf
> 
> Best,
>  Carsten
> 
> > On 26 May 2016, at 10:19, Maximilien LOPES RODRIGUES 
> >  wrote:
> > 
> > Dear GROMACS users,
> > 
> > first of all, thank you for paying attention to my question.
> > 
> > I have a system containing a membrane protein (porin) that is embedded in a 
> > lipid bilayer (XY).
> > I would like to investigate the flux of ions (or other solutes like sugar) 
> > that can pass through the protein.
> > Unfortunately, I don't know the general rules to make a such simulation.
> > 
> > - Can I just add a higher concentration of ions in one side ? (if yes, 
> > should I suppress PBC in Z axis ?)
> > - Do I put the counter ions on the same side ?
> > - So, do I have to make PBC condition only on XY plan ?
> > - Is there an external electrical field to apply ? If yes, how ?
> > 
> > If you have general tutorial documentation, I would be happy to take a look 
> > at it !
> > 
> > Thank you !
> > Kind regards,
> > Maximilien Lopes Rodrigues
> > 
> > -- 
> > 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] Extending the MD

[SAPNA BORAH]

:)

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Thu, May 26, 2016 at 6:01 PM, sun  wrote:

> Allright Sapna. Thank you very much.
>
> Sent from my iPhone
>
> > On 26-May-2016, at 4:59 pm, SAPNA BORAH  wrote:
> >
> > I would suggest if you want simulation runs with new name, add the
> -deffnm
> > switch and provide the default name :)
> > Saves us from all the trouble to rename the files all over again.
> >
> > gmx mdrun -v -s next1.tpr -cpi state.cpt -deffnm new
> >
> >
> > Sapna Mayuri Borah
> > c/o Dr. A. N. Jha
> > Research student
> > Tezpur University,
> > India
> >
> >> On Thu, May 26, 2016 at 4:57 PM, SAPNA BORAH 
> wrote:
> >>
> >> It may be a case. You can rename the files to what they were and try
> >> again. Since here, the error simply implies the files are renamed or
> >> missing.
> >>
> >> Sapna Mayuri Borah
> >> c/o Dr. A. N. Jha
> >> Research student
> >> Tezpur University,
> >> India
> >>
> >>> On Thu, May 26, 2016 at 4:46 PM, sun  wrote:
> >>>
> >>> Yes
> >>> In my case it was state.cpt and used the following command after
> >>> generating .tpr:
> >>> gmx mdrun -v -s next1.tpr -cpi state.cpt
> >>>
> >>> Has it anything to do with trajectory or log files generated in 100 ns
> >>> case? I have renamed the .trr and .xtc files generated for 100 ns
> >>> simulation.
> >>>
> >>> Sent from my iPhone
> >>>
>  On 26-May-2016, at 4:43 pm, SAPNA BORAH 
> wrote:
> 
>  Well that's kinda new i must say. Can you please paste the entire
> >>> command
>  you have used. I think you have mis-named the file :).
> 
>  By previous.cpt, I mean your last/previous checkpoint file of the
>  simulation run, that will be state.cpt in your case.. Hope you have
>  mentioned that. Ignore if you have :)
> 
>  Sapna Mayuri Borah
>  c/o Dr. A. N. Jha
>  Research student
>  Tezpur University,
>  India
> 
> > On Thu, May 26, 2016 at 4:38 PM, sun  wrote:
> >
> > Hello Sapna
> > I tried adding previous.cpt but the following the following error
> >>> appears:
> > "One out of the 4 files is either missing or renamed"
> >
> >
> >
> > Sent from my iPhone
> >
> >> On 26-May-2016, at 4:35 pm, SAPNA BORAH 
> >>> wrote:
> >>
> >> Hi!!
> >>
> >> After converting the tpr, while initiating mdrun, try adding the
> >>> previous
> >> cpt file as well..
> >>
> >> mdrun -s next.tpr -cpi previous.cpt
> >>
> >> Thanks!
> >>
> >>
> >> Sapna Mayuri Borah
> >> c/o Dr. A. N. Jha
> >> Research student
> >> Tezpur University,
> >> India
> >>
> >>> On Thu, May 26, 2016 at 4:31 PM, sun  wrote:
> >>>
> >>> Hello
> >>> I started a 100 ns ns pro-lig simulation which was terminated
> >>> accidently
> >>> at 53.33 ns. Then I restarted simulation with checkpoint file and
> >>> simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr
> >>> files
> >>> which were generated for 53.33 and 100 ns data reapectively and
> log,
> >>> trr
> >>> file for both 53.33 and 100 ns MD. I have state.cpt,
> state_prev.cpt,
> >>> md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i
> >>> gave
> > the
> >>> following commands:
> >>> gmx convert-tpr -f md_0_1.tpr -extend 20 -o next1.tpr
> >>> and
> >>> gmx mdrun -v next1.tpr
> >>>
> >>> But, the mdrun started from initial step and time 0.00. That means
> >>> simulation is starting from begining and not after 100 ns to 200
> ns.
> >>> I
> > am
> >>> confused if i am using the right .tpr file or shall I use
> checkpoint
> > file.
> >>> Same results are obtained when i used next.tpr instead of
> md_0_1.tpr.
> > When
> >>> i used checkpoint files (all three files in three different steps)
> >>> the
> >>> simulation is starting from 53.33 ns. Plz suggest where I am going
> > wrong.
> >>> With Regards
> >>> Suniba
> >>>
> >>> Sent from my iPhone
> >>> --
> >>> 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.
> >> --
> >> 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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> >>
> >> * For 

Re: [gmx-users] Extending the MD

[sun]

Allright Sapna. Thank you very much.

Sent from my iPhone

> On 26-May-2016, at 4:59 pm, SAPNA BORAH  wrote:
> 
> I would suggest if you want simulation runs with new name, add the -deffnm
> switch and provide the default name :)
> Saves us from all the trouble to rename the files all over again.
> 
> gmx mdrun -v -s next1.tpr -cpi state.cpt -deffnm new
> 
> 
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
> 
>> On Thu, May 26, 2016 at 4:57 PM, SAPNA BORAH  wrote:
>> 
>> It may be a case. You can rename the files to what they were and try
>> again. Since here, the error simply implies the files are renamed or
>> missing.
>> 
>> Sapna Mayuri Borah
>> c/o Dr. A. N. Jha
>> Research student
>> Tezpur University,
>> India
>> 
>>> On Thu, May 26, 2016 at 4:46 PM, sun  wrote:
>>> 
>>> Yes
>>> In my case it was state.cpt and used the following command after
>>> generating .tpr:
>>> gmx mdrun -v -s next1.tpr -cpi state.cpt
>>> 
>>> Has it anything to do with trajectory or log files generated in 100 ns
>>> case? I have renamed the .trr and .xtc files generated for 100 ns
>>> simulation.
>>> 
>>> Sent from my iPhone
>>> 
 On 26-May-2016, at 4:43 pm, SAPNA BORAH  wrote:
 
 Well that's kinda new i must say. Can you please paste the entire
>>> command
 you have used. I think you have mis-named the file :).
 
 By previous.cpt, I mean your last/previous checkpoint file of the
 simulation run, that will be state.cpt in your case.. Hope you have
 mentioned that. Ignore if you have :)
 
 Sapna Mayuri Borah
 c/o Dr. A. N. Jha
 Research student
 Tezpur University,
 India
 
> On Thu, May 26, 2016 at 4:38 PM, sun  wrote:
> 
> Hello Sapna
> I tried adding previous.cpt but the following the following error
>>> appears:
> "One out of the 4 files is either missing or renamed"
> 
> 
> 
> Sent from my iPhone
> 
>> On 26-May-2016, at 4:35 pm, SAPNA BORAH 
>>> wrote:
>> 
>> Hi!!
>> 
>> After converting the tpr, while initiating mdrun, try adding the
>>> previous
>> cpt file as well..
>> 
>> mdrun -s next.tpr -cpi previous.cpt
>> 
>> Thanks!
>> 
>> 
>> Sapna Mayuri Borah
>> c/o Dr. A. N. Jha
>> Research student
>> Tezpur University,
>> India
>> 
>>> On Thu, May 26, 2016 at 4:31 PM, sun  wrote:
>>> 
>>> Hello
>>> I started a 100 ns ns pro-lig simulation which was terminated
>>> accidently
>>> at 53.33 ns. Then I restarted simulation with checkpoint file and
>>> simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr
>>> files
>>> which were generated for 53.33 and 100 ns data reapectively and log,
>>> trr
>>> file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt,
>>> md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i
>>> gave
> the
>>> following commands:
>>> gmx convert-tpr -f md_0_1.tpr -extend 20 -o next1.tpr
>>> and
>>> gmx mdrun -v next1.tpr
>>> 
>>> But, the mdrun started from initial step and time 0.00. That means
>>> simulation is starting from begining and not after 100 ns to 200 ns.
>>> I
> am
>>> confused if i am using the right .tpr file or shall I use checkpoint
> file.
>>> Same results are obtained when i used next.tpr instead of md_0_1.tpr.
> When
>>> i used checkpoint files (all three files in three different steps)
>>> the
>>> simulation is starting from 53.33 ns. Plz suggest where I am going
> wrong.
>>> With Regards
>>> Suniba
>>> 
>>> Sent from my iPhone
>>> --
>>> 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.
>> --
>> 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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> 
> * For 

Re: [gmx-users] simulation_time[Nikita Bora]

[Justin Lemkul]

On 5/26/16 7:16 AM, SAPNA BORAH wrote:

That seems quite clear nw.. thanks.. :)
so a slight deviation from values rvdw=1.4 to rvdw=1 and r coulomb=1.4 to r
coulomb=1
wont matter much unless its experimentally validated



That's not a "slight" difference and can, in fact, undermine the entire 
nonbonded setup.  The net takeaway from this discussion (and all of the previous 
ones on this topic) should be as follows:


1. The water model should be regarded as part of the force field; specific 
applications (validated in the literature) may permit non-default selections.


2. The nonbonded setup is the most critical thing to get right; again, this is 
not something that you can assume is going to make a small difference.  It can, 
in fact, ruin everything if not properly set up.  We spend years of our lives 
getting these force fields right, within certain operating parameters and 
assumptions, only to have users assume they know better by trying to speed 
things up (reducing cutoffs) or "be more accurate" (increasing cutoffs), neither 
of which is legitimate.


3. Before touching anything, the user should investigate the chosen force field 
- its origins, assumptions, previous applications, criticisms and revisions, 
etc. that are published.  If the user has not done this, how can he/she justify 
that the force field should even be used?  If you don't know the cutoffs, did 
you go back and read about the force field, or are you trusting on blind faith 
that existing hand-me-down protocols are correct, or that stuff you read in 
tutorials/mailing lists/random Internet posts are actually scientifically valid?


There's a lot of homework that should be done before ever running a simulation, 
and it's real science, not just some arbitrary set of numbers you can concoct. 
You wouldn't walk into a chemistry lab and mix two clear liquids together 
because they look pretty much the same, would you? ;)


-Justin


Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Thu, May 26, 2016 at 1:59 PM, Mark Abraham 
wrote:


Hi,

A report written by the people who designed the method that describes how
they used it *is* a direct way to know the values to use. People they often
publish with are also probably pretty reliable. Even better still are the
people who show why their parameter choices work. The models didn't arrive
by divine inspiration :-)

Mark

On Thu, May 26, 2016 at 8:42 AM SAPNA BORAH 
wrote:


hi...
So there is no direct way to know the values to be used .
however the last line is still unclear...


Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Fri, May 20, 2016 at 12:00 PM, Tsjerk Wassenaar 
wrote:


Hi Nikita,

It's not like there's a range to take a minimum from. It's this with

this

force field and that with another. Any deviation will alter the

behaviour

of the force field, and you'll have to show that the result is valid,
either by running tests, or by referring to a paper that has results

from

such tests. The most suitable value is probably the one used by groups

that

have direct ties to the developing group(s).


Hope it helps,


Tsjerk



On May 20, 2016 07:20, "Ms. Nikita Bora"  wrote:


Thanks Tsjerk

That was really a good explanation. And it helped me out a lot.
Still,I would like to know what are the standard values for these
parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used.

As earlier it was mentioned that with different force field different
value is used so is there any link where i can get to know the

minimum

cut

off values for these parameters and which value should be used for

which

force field or condition

thanks
Nikita



  Original Message



Subject: Re: simulation_time
From:"Ms. Nikita Bora" 
Date:Mon, May 16, 2016 9:42 am
To:  nik...@tezu.ernet.in








--


Respected Sir,

Thanks for the reply. I would further like to know that according

to

this

tutorial
(







http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html

)

the rvdw=rcoulomb=1 is used for the protein while according to this
tutorial
(







http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html

)

rvdw=rcoulomb=1.4 is used. why a different value for the simple

protein

and protein-ligand complex is used??



Different force fields, different settings.

-Justin






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Re: [gmx-users] Calculate total non-bonded contacts in gromacs

[Justin Lemkul]

On 5/26/16 6:31 AM, SAPNA BORAH wrote:

Dear all,

Is there any protocol in gromacs that can help me get the total number of
non-bonded contacts in a protein, or protein-ligand with respect to time?



gmx mindist -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 629
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] Extending the MD

[SAPNA BORAH]

I would suggest if you want simulation runs with new name, add the -deffnm
switch and provide the default name :)
Saves us from all the trouble to rename the files all over again.

gmx mdrun -v -s next1.tpr -cpi state.cpt -deffnm new


Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Thu, May 26, 2016 at 4:57 PM, SAPNA BORAH  wrote:

> It may be a case. You can rename the files to what they were and try
> again. Since here, the error simply implies the files are renamed or
> missing.
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
>
> On Thu, May 26, 2016 at 4:46 PM, sun  wrote:
>
>> Yes
>> In my case it was state.cpt and used the following command after
>> generating .tpr:
>> gmx mdrun -v -s next1.tpr -cpi state.cpt
>>
>> Has it anything to do with trajectory or log files generated in 100 ns
>> case? I have renamed the .trr and .xtc files generated for 100 ns
>> simulation.
>>
>> Sent from my iPhone
>>
>> > On 26-May-2016, at 4:43 pm, SAPNA BORAH  wrote:
>> >
>> > Well that's kinda new i must say. Can you please paste the entire
>> command
>> > you have used. I think you have mis-named the file :).
>> >
>> > By previous.cpt, I mean your last/previous checkpoint file of the
>> > simulation run, that will be state.cpt in your case.. Hope you have
>> > mentioned that. Ignore if you have :)
>> >
>> > Sapna Mayuri Borah
>> > c/o Dr. A. N. Jha
>> > Research student
>> > Tezpur University,
>> > India
>> >
>> >> On Thu, May 26, 2016 at 4:38 PM, sun  wrote:
>> >>
>> >> Hello Sapna
>> >> I tried adding previous.cpt but the following the following error
>> appears:
>> >> "One out of the 4 files is either missing or renamed"
>> >>
>> >>
>> >>
>> >> Sent from my iPhone
>> >>
>> >>> On 26-May-2016, at 4:35 pm, SAPNA BORAH 
>> wrote:
>> >>>
>> >>> Hi!!
>> >>>
>> >>> After converting the tpr, while initiating mdrun, try adding the
>> previous
>> >>> cpt file as well..
>> >>>
>> >>> mdrun -s next.tpr -cpi previous.cpt
>> >>>
>> >>> Thanks!
>> >>>
>> >>>
>> >>> Sapna Mayuri Borah
>> >>> c/o Dr. A. N. Jha
>> >>> Research student
>> >>> Tezpur University,
>> >>> India
>> >>>
>>  On Thu, May 26, 2016 at 4:31 PM, sun  wrote:
>> 
>>  Hello
>>  I started a 100 ns ns pro-lig simulation which was terminated
>> accidently
>>  at 53.33 ns. Then I restarted simulation with checkpoint file and
>>  simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr
>> files
>>  which were generated for 53.33 and 100 ns data reapectively and log,
>> trr
>>  file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt,
>>  md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i
>> gave
>> >> the
>>  following commands:
>>  gmx convert-tpr -f md_0_1.tpr -extend 20 -o next1.tpr
>>  and
>>  gmx mdrun -v next1.tpr
>> 
>>  But, the mdrun started from initial step and time 0.00. That means
>>  simulation is starting from begining and not after 100 ns to 200 ns.
>> I
>> >> am
>>  confused if i am using the right .tpr file or shall I use checkpoint
>> >> file.
>>  Same results are obtained when i used next.tpr instead of md_0_1.tpr.
>> >> When
>>  i used checkpoint files (all three files in three different steps)
>> the
>>  simulation is starting from 53.33 ns. Plz suggest where I am going
>> >> wrong.
>>  With Regards
>>  Suniba
>> 
>>  Sent from my iPhone
>>  --
>>  Gromacs Users mailing list
>> 
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>>  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] Extending the MD

[SAPNA BORAH]

It may be a case. You can rename the files to what they were and try again.
Since here, the error simply implies the files are renamed or missing.

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Thu, May 26, 2016 at 4:46 PM, sun  wrote:

> Yes
> In my case it was state.cpt and used the following command after
> generating .tpr:
> gmx mdrun -v -s next1.tpr -cpi state.cpt
>
> Has it anything to do with trajectory or log files generated in 100 ns
> case? I have renamed the .trr and .xtc files generated for 100 ns
> simulation.
>
> Sent from my iPhone
>
> > On 26-May-2016, at 4:43 pm, SAPNA BORAH  wrote:
> >
> > Well that's kinda new i must say. Can you please paste the entire command
> > you have used. I think you have mis-named the file :).
> >
> > By previous.cpt, I mean your last/previous checkpoint file of the
> > simulation run, that will be state.cpt in your case.. Hope you have
> > mentioned that. Ignore if you have :)
> >
> > Sapna Mayuri Borah
> > c/o Dr. A. N. Jha
> > Research student
> > Tezpur University,
> > India
> >
> >> On Thu, May 26, 2016 at 4:38 PM, sun  wrote:
> >>
> >> Hello Sapna
> >> I tried adding previous.cpt but the following the following error
> appears:
> >> "One out of the 4 files is either missing or renamed"
> >>
> >>
> >>
> >> Sent from my iPhone
> >>
> >>> On 26-May-2016, at 4:35 pm, SAPNA BORAH 
> wrote:
> >>>
> >>> Hi!!
> >>>
> >>> After converting the tpr, while initiating mdrun, try adding the
> previous
> >>> cpt file as well..
> >>>
> >>> mdrun -s next.tpr -cpi previous.cpt
> >>>
> >>> Thanks!
> >>>
> >>>
> >>> Sapna Mayuri Borah
> >>> c/o Dr. A. N. Jha
> >>> Research student
> >>> Tezpur University,
> >>> India
> >>>
>  On Thu, May 26, 2016 at 4:31 PM, sun  wrote:
> 
>  Hello
>  I started a 100 ns ns pro-lig simulation which was terminated
> accidently
>  at 53.33 ns. Then I restarted simulation with checkpoint file and
>  simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr
> files
>  which were generated for 53.33 and 100 ns data reapectively and log,
> trr
>  file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt,
>  md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i gave
> >> the
>  following commands:
>  gmx convert-tpr -f md_0_1.tpr -extend 20 -o next1.tpr
>  and
>  gmx mdrun -v next1.tpr
> 
>  But, the mdrun started from initial step and time 0.00. That means
>  simulation is starting from begining and not after 100 ns to 200 ns. I
> >> am
>  confused if i am using the right .tpr file or shall I use checkpoint
> >> file.
>  Same results are obtained when i used next.tpr instead of md_0_1.tpr.
> >> When
>  i used checkpoint files (all three files in three different steps) the
>  simulation is starting from 53.33 ns. Plz suggest where I am going
> >> wrong.
>  With Regards
>  Suniba
> 
>  Sent from my iPhone
>  --
>  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] simulation_time[Nikita Bora]

[SAPNA BORAH]

That seems quite clear nw.. thanks.. :)
so a slight deviation from values rvdw=1.4 to rvdw=1 and r coulomb=1.4 to r
coulomb=1
wont matter much unless its experimentally validated

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Thu, May 26, 2016 at 1:59 PM, Mark Abraham 
wrote:

> Hi,
>
> A report written by the people who designed the method that describes how
> they used it *is* a direct way to know the values to use. People they often
> publish with are also probably pretty reliable. Even better still are the
> people who show why their parameter choices work. The models didn't arrive
> by divine inspiration :-)
>
> Mark
>
> On Thu, May 26, 2016 at 8:42 AM SAPNA BORAH 
> wrote:
>
> > hi...
> > So there is no direct way to know the values to be used .
> > however the last line is still unclear...
> >
> >
> > Sapna Mayuri Borah
> > c/o Dr. A. N. Jha
> > Research student
> > Tezpur University,
> > India
> >
> > On Fri, May 20, 2016 at 12:00 PM, Tsjerk Wassenaar 
> > wrote:
> >
> > > Hi Nikita,
> > >
> > > It's not like there's a range to take a minimum from. It's this with
> this
> > > force field and that with another. Any deviation will alter the
> behaviour
> > > of the force field, and you'll have to show that the result is valid,
> > > either by running tests, or by referring to a paper that has results
> from
> > > such tests. The most suitable value is probably the one used by groups
> > that
> > > have direct ties to the developing group(s).
> > >
> > >
> > > Hope it helps,
> > >
> > >
> > > Tsjerk
> > >
> > >
> > >
> > > On May 20, 2016 07:20, "Ms. Nikita Bora"  wrote:
> > >
> > > > Thanks Tsjerk
> > > >
> > > > That was really a good explanation. And it helped me out a lot.
> > > > Still,I would like to know what are the standard values for these
> > > > parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used.
> > > >
> > > > As earlier it was mentioned that with different force field different
> > > > value is used so is there any link where i can get to know the
> minimum
> > > cut
> > > > off values for these parameters and which value should be used for
> > which
> > > > force field or condition
> > > >
> > > > thanks
> > > > Nikita
> > > >
> > > >
> > > >
> > > >   Original Message
> > > 
> > > > > Subject: Re: simulation_time
> > > > > From:"Ms. Nikita Bora" 
> > > > > Date:Mon, May 16, 2016 9:42 am
> > > > > To:  nik...@tezu.ernet.in
> > > > >
> > > >
> > >
> >
> --
> > > > >
> > > > > Respected Sir,
> > > > >
> > > > > Thanks for the reply. I would further like to know that according
> to
> > > this
> > > > > tutorial
> > > > > (
> > > >
> > >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> > > > )
> > > > > the rvdw=rcoulomb=1 is used for the protein while according to this
> > > > > tutorial
> > > > > (
> > > >
> > >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> > > > )
> > > > > rvdw=rcoulomb=1.4 is used. why a different value for the simple
> > protein
> > > > > and protein-ligand complex is used??
> > > > >
> > > >
> > > > Different force fields, different settings.
> > > >
> > > > -Justin
> > > >
> > > > >
> > > >
> > > >
> > > > ___
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Re: [gmx-users] Extending the MD

[sun]

Yes
In my case it was state.cpt and used the following command after generating 
.tpr:
gmx mdrun -v -s next1.tpr -cpi state.cpt

Has it anything to do with trajectory or log files generated in 100 ns case? I 
have renamed the .trr and .xtc files generated for 100 ns simulation. 

Sent from my iPhone

> On 26-May-2016, at 4:43 pm, SAPNA BORAH  wrote:
> 
> Well that's kinda new i must say. Can you please paste the entire command
> you have used. I think you have mis-named the file :).
> 
> By previous.cpt, I mean your last/previous checkpoint file of the
> simulation run, that will be state.cpt in your case.. Hope you have
> mentioned that. Ignore if you have :)
> 
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
> 
>> On Thu, May 26, 2016 at 4:38 PM, sun  wrote:
>> 
>> Hello Sapna
>> I tried adding previous.cpt but the following the following error appears:
>> "One out of the 4 files is either missing or renamed"
>> 
>> 
>> 
>> Sent from my iPhone
>> 
>>> On 26-May-2016, at 4:35 pm, SAPNA BORAH  wrote:
>>> 
>>> Hi!!
>>> 
>>> After converting the tpr, while initiating mdrun, try adding the previous
>>> cpt file as well..
>>> 
>>> mdrun -s next.tpr -cpi previous.cpt
>>> 
>>> Thanks!
>>> 
>>> 
>>> Sapna Mayuri Borah
>>> c/o Dr. A. N. Jha
>>> Research student
>>> Tezpur University,
>>> India
>>> 
 On Thu, May 26, 2016 at 4:31 PM, sun  wrote:
 
 Hello
 I started a 100 ns ns pro-lig simulation which was terminated accidently
 at 53.33 ns. Then I restarted simulation with checkpoint file and
 simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr files
 which were generated for 53.33 and 100 ns data reapectively and log, trr
 file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt,
 md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i gave
>> the
 following commands:
 gmx convert-tpr -f md_0_1.tpr -extend 20 -o next1.tpr
 and
 gmx mdrun -v next1.tpr
 
 But, the mdrun started from initial step and time 0.00. That means
 simulation is starting from begining and not after 100 ns to 200 ns. I
>> am
 confused if i am using the right .tpr file or shall I use checkpoint
>> file.
 Same results are obtained when i used next.tpr instead of md_0_1.tpr.
>> When
 i used checkpoint files (all three files in three different steps) the
 simulation is starting from 53.33 ns. Plz suggest where I am going
>> wrong.
 With Regards
 Suniba
 
 Sent from my iPhone
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Re: [gmx-users] Extending the MD

[SAPNA BORAH]

Well that's kinda new i must say. Can you please paste the entire command
you have used. I think you have mis-named the file :).

By previous.cpt, I mean your last/previous checkpoint file of the
simulation run, that will be state.cpt in your case.. Hope you have
mentioned that. Ignore if you have :)

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Thu, May 26, 2016 at 4:38 PM, sun  wrote:

> Hello Sapna
> I tried adding previous.cpt but the following the following error appears:
> "One out of the 4 files is either missing or renamed"
>
>
>
> Sent from my iPhone
>
> > On 26-May-2016, at 4:35 pm, SAPNA BORAH  wrote:
> >
> > Hi!!
> >
> > After converting the tpr, while initiating mdrun, try adding the previous
> > cpt file as well..
> >
> > mdrun -s next.tpr -cpi previous.cpt
> >
> > Thanks!
> >
> >
> > Sapna Mayuri Borah
> > c/o Dr. A. N. Jha
> > Research student
> > Tezpur University,
> > India
> >
> >> On Thu, May 26, 2016 at 4:31 PM, sun  wrote:
> >>
> >> Hello
> >> I started a 100 ns ns pro-lig simulation which was terminated accidently
> >> at 53.33 ns. Then I restarted simulation with checkpoint file and
> >> simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr files
> >> which were generated for 53.33 and 100 ns data reapectively and log, trr
> >> file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt,
> >> md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i gave
> the
> >> following commands:
> >> gmx convert-tpr -f md_0_1.tpr -extend 20 -o next1.tpr
> >> and
> >> gmx mdrun -v next1.tpr
> >>
> >> But, the mdrun started from initial step and time 0.00. That means
> >> simulation is starting from begining and not after 100 ns to 200 ns. I
> am
> >> confused if i am using the right .tpr file or shall I use checkpoint
> file.
> >> Same results are obtained when i used next.tpr instead of md_0_1.tpr.
> When
> >> i used checkpoint files (all three files in three different steps) the
> >> simulation is starting from 53.33 ns. Plz suggest where I am going
> wrong.
> >> With Regards
> >> Suniba
> >>
> >> Sent from my iPhone
> >> --
> >> 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] Extending the MD

[sun]

Hello Sapna
I tried adding previous.cpt but the following the following error appears: 
"One out of the 4 files is either missing or renamed"



Sent from my iPhone

> On 26-May-2016, at 4:35 pm, SAPNA BORAH  wrote:
> 
> Hi!!
> 
> After converting the tpr, while initiating mdrun, try adding the previous
> cpt file as well..
> 
> mdrun -s next.tpr -cpi previous.cpt
> 
> Thanks!
> 
> 
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
> 
>> On Thu, May 26, 2016 at 4:31 PM, sun  wrote:
>> 
>> Hello
>> I started a 100 ns ns pro-lig simulation which was terminated accidently
>> at 53.33 ns. Then I restarted simulation with checkpoint file and
>> simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr files
>> which were generated for 53.33 and 100 ns data reapectively and log, trr
>> file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt,
>> md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i gave the
>> following commands:
>> gmx convert-tpr -f md_0_1.tpr -extend 20 -o next1.tpr
>> and
>> gmx mdrun -v next1.tpr
>> 
>> But, the mdrun started from initial step and time 0.00. That means
>> simulation is starting from begining and not after 100 ns to 200 ns. I am
>> confused if i am using the right .tpr file or shall I use checkpoint file.
>> Same results are obtained when i used next.tpr instead of md_0_1.tpr. When
>> i used checkpoint files (all three files in three different steps) the
>> simulation is starting from 53.33 ns. Plz suggest where I am going wrong.
>> With Regards
>> Suniba
>> 
>> Sent from my iPhone
>> --
>> Gromacs Users mailing list
>> 
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Re: [gmx-users] Extending the MD

[SAPNA BORAH]

Hi!!

After converting the tpr, while initiating mdrun, try adding the previous
cpt file as well..

mdrun -s next.tpr -cpi previous.cpt

Thanks!


Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Thu, May 26, 2016 at 4:31 PM, sun  wrote:

> Hello
> I started a 100 ns ns pro-lig simulation which was terminated accidently
> at 53.33 ns. Then I restarted simulation with checkpoint file and
> simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr files
> which were generated for 53.33 and 100 ns data reapectively and log, trr
> file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt,
> md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i gave the
> following commands:
> gmx convert-tpr -f md_0_1.tpr -extend 20 -o next1.tpr
> and
> gmx mdrun -v next1.tpr
>
> But, the mdrun started from initial step and time 0.00. That means
> simulation is starting from begining and not after 100 ns to 200 ns. I am
> confused if i am using the right .tpr file or shall I use checkpoint file.
> Same results are obtained when i used next.tpr instead of md_0_1.tpr. When
> i used checkpoint files (all three files in three different steps) the
> simulation is starting from 53.33 ns. Plz suggest where I am going wrong.
> With Regards
> Suniba
>
> Sent from my iPhone
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[gmx-users] Extending the MD

[sun]

Hello 
I started a 100 ns ns pro-lig simulation which was terminated accidently at 
53.33 ns. Then I restarted simulation with checkpoint file and simulation ended 
at 100 ns. Now I have the md_0_1.tpr and next.tpr files which were generated 
for 53.33 and 100 ns data reapectively and log, trr file for both 53.33 and 100 
ns MD. I have state.cpt, state_prev.cpt, md_0_1.cpt. Now i want to extend the 
simulation upto 200 ns. So i gave the following commands:
gmx convert-tpr -f md_0_1.tpr -extend 20 -o next1.tpr
and
gmx mdrun -v next1.tpr

But, the mdrun started from initial step and time 0.00. That means simulation 
is starting from begining and not after 100 ns to 200 ns. I am confused if i am 
using the right .tpr file or shall I use checkpoint file. Same results are 
obtained when i used next.tpr instead of md_0_1.tpr. When i used checkpoint 
files (all three files in three different steps) the simulation is starting 
from 53.33 ns. Plz suggest where I am going wrong. 
With Regards
Suniba

Sent from my iPhone
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[gmx-users] Calculate total non-bonded contacts in gromacs

[SAPNA BORAH]

Dear all,

Is there any protocol in gromacs that can help me get the total number of
non-bonded contacts in a protein, or protein-ligand with respect to time?

Thanks in advance.

Regards,
Sapna.


Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India
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[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

[Antara mazumdar]

Dear Mark,

Thanks for the suggestion. I will tell them that.
Kind Regards,
Antara

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Re: [gmx-users] Installing GROMACS 5.1.2 om GPU

[Mark Abraham]

Hi,

So did you try the other half of my suggestion? (And ask harder -
installing gcc is no harder than installing icc, and there is no point
buying CUDA GPUs without funding for people to install compilers that
support them.)

Mark

‪On Thu, May 26, 2016 at 11:39 AM ‫יוכבד‬‎  wrote:‬

> The problem is the gcc installed on our cluster is to old and it is not
> possible to upgrade at the moment.
>
> On Wed, May 25, 2016 at 1:44 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> You need to follow Intel's instructions for accessing the compiler -
>> including running their magic scripts from each shell that you want to
>> compile from. (Or save yourself some pain, use gcc, and probably run
>> slightly faster.)
>>
>> Mark
>>
>> ‪On Wed, May 25, 2016 at 10:43 AM ‫יוכבד‬‎  wrote:‬
>>
>>> Hi
>>>
>>> I've been having lots of trouble installing gromacs on our GPU machine.
>>>
>>> I have Intel2015 Compilers on my machine which are identified correctly
>>> during configuration.
>>>
>>> /private/gnss/cmake-2.8.11.2/bin/cmake ..
>>> -DCMAKE_INSTALL_PREFIX=/private/gnss/gromacs-5.1.2
>>> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5/
>>> -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_FFT_LIBRARY=mkl
>>> -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include
>>>
>>> However when I run the make I get alot of warnings and finally the
>>> following error:
>>>
>>> /private/gnss/gromacs-5.1.2/src/external/boost/boost/config/compiler/in
>>> tel.hpp(93): remark #193: zero used for undefined preprocessing
>>> identifier
>>> "_WCHAR_T_DEFINED"
>>> # if ((_WCHAR_T_DEFINED + 0) == 0) && ((_WCHAR_T + 0) == 0)
>>> ^
>>>
>>> Linking CXX executable ../../bin/template
>>> ld: warning: libimf.so, needed by ../../lib/libgromacs.so.1.2.0, not
>>> found
>>> (try using -rpath or -rpath-link)
>>> ld: warning: libsvml.so, needed by ../../lib/libgromacs.so.1.2.0, not
>>> found
>>> (try using -rpath or -rpath-link)
>>> ld: warning: libirng.so, needed by ../../lib/libgromacs.so.1.2.0, not
>>> found
>>> (try using -rpath or -rpath-link)
>>> ld: warning: libintlc.so.5, needed by ../../lib/libgromacs.so.1.2.0, not
>>> found (try using -rpath or -rpath-link)
>>> ld: ../../bin/template: hidden symbol `__intel_cpu_features_init_x' in
>>>
>>> /opt/intel/composer_xe_2015.5.223/compiler/lib/intel64/libirc.a(cpu_feature_disp.o)
>>> is referenced by DSO
>>> ld: final link failed: Nonrepresentable section on output
>>> make[2]: *** [bin/template] Error 1
>>> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>> all the files which are not found do exist in the compiler libraries and
>>> it
>>> is added to my path.
>>>
>>> Any suggestions how to solve this?
>>>
>>> Thanks
>>>
>>> Yocheved
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
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>>
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Re: [gmx-users] Installing GROMACS 5.1.2 om GPU

[יוכבד]

The problem is the gcc installed on our cluster is to old and it is not
possible to upgrade at the moment.

On Wed, May 25, 2016 at 1:44 PM, Mark Abraham 
wrote:

> Hi,
>
> You need to follow Intel's instructions for accessing the compiler -
> including running their magic scripts from each shell that you want to
> compile from. (Or save yourself some pain, use gcc, and probably run
> slightly faster.)
>
> Mark
>
> ‪On Wed, May 25, 2016 at 10:43 AM ‫יוכבד‬‎  wrote:‬
>
>> Hi
>>
>> I've been having lots of trouble installing gromacs on our GPU machine.
>>
>> I have Intel2015 Compilers on my machine which are identified correctly
>> during configuration.
>>
>> /private/gnss/cmake-2.8.11.2/bin/cmake ..
>> -DCMAKE_INSTALL_PREFIX=/private/gnss/gromacs-5.1.2
>> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5/
>> -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_FFT_LIBRARY=mkl
>> -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include
>>
>> However when I run the make I get alot of warnings and finally the
>> following error:
>>
>> /private/gnss/gromacs-5.1.2/src/external/boost/boost/config/compiler/in
>> tel.hpp(93): remark #193: zero used for undefined preprocessing identifier
>> "_WCHAR_T_DEFINED"
>> # if ((_WCHAR_T_DEFINED + 0) == 0) && ((_WCHAR_T + 0) == 0)
>> ^
>>
>> Linking CXX executable ../../bin/template
>> ld: warning: libimf.so, needed by ../../lib/libgromacs.so.1.2.0, not found
>> (try using -rpath or -rpath-link)
>> ld: warning: libsvml.so, needed by ../../lib/libgromacs.so.1.2.0, not
>> found
>> (try using -rpath or -rpath-link)
>> ld: warning: libirng.so, needed by ../../lib/libgromacs.so.1.2.0, not
>> found
>> (try using -rpath or -rpath-link)
>> ld: warning: libintlc.so.5, needed by ../../lib/libgromacs.so.1.2.0, not
>> found (try using -rpath or -rpath-link)
>> ld: ../../bin/template: hidden symbol `__intel_cpu_features_init_x' in
>>
>> /opt/intel/composer_xe_2015.5.223/compiler/lib/intel64/libirc.a(cpu_feature_disp.o)
>> is referenced by DSO
>> ld: final link failed: Nonrepresentable section on output
>> make[2]: *** [bin/template] Error 1
>> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> make: *** [all] Error 2
>>
>> all the files which are not found do exist in the compiler libraries and
>> it
>> is added to my path.
>>
>> Any suggestions how to solve this?
>>
>> Thanks
>>
>> Yocheved
>> --
>> Gromacs Users mailing list
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>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>>
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[gmx-users] gmx gangle failure after assigning zero-charges

[Thomas Niklas]

Hi there,
I have been using GROMACS version 5.0.6 to perform some simple MD 
Simulations that involve a polystyrene strand and a single further 
molecule (e.g. toluene). I wanted to observe some angles between both 
molecules so after I produced a trajectory, I applied "gmx gangle" and 
everything worked just perfectly. I subsequently employed a topology in 
which I did not change anything except that I assigned zero-charges 
(instead of standard OPLS-AA values) to all atoms and produced another 
trajectory.

In this case analysis with "gmx gangle" immediately aborts with:

.../gromacs-5.0.6/src/gromacs/gmxlib/pbc.c, line: 81

Fatal error:
Unknown ePBC=38063816 in ePBC2npbcdim

I am following basic procedures with these simulations, since I have not 
much experience in MD. However, I think this is a bit odd and probably 
not my fault? I further guess that, since I have trajectories, I can 
also utilize something like vmd or travis to also get the angles I am 
interested in?

Thank you and best regards,
Thomas Niklas
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Re: [gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

[Mark Abraham]

Hi,

Oh, and get them to install it properly. You should not be running from
.../build/bin

Mark

On Thu, May 26, 2016 at 10:54 AM Antara mazumdar 
wrote:

> Dear Mark,
>
>I will ask our HPC support team to check the MPI enabled version of
> gromacs then. Thank you for your suggestion.
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
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[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

[Antara mazumdar]

Dear Mark,

   I will ask our HPC support team to check the MPI enabled version of
gromacs then. Thank you for your suggestion.
Kind Regards,
Antara

--
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Re: [gmx-users] Ion flux through membrane protein

[Kutzner, Carsten]

Hi Maximilien,

depending on what exactly the questions are that you like to address, the 
double-membrane
setup as used in computational electrophysiology setups might be helpful for 
you.
There is a section in the GROMACS PDF manual about that, and there are these 
two papers:
http://www.sciencedirect.com/science/article/pii/S0005273616300360
http://www.mpibpc.mpg.de/275657/Kutzner_2011_BPJ_101_809-817.pdf

Best,
 Carsten

> On 26 May 2016, at 10:19, Maximilien LOPES RODRIGUES 
>  wrote:
> 
> Dear GROMACS users,
> 
> first of all, thank you for paying attention to my question.
> 
> I have a system containing a membrane protein (porin) that is embedded in a 
> lipid bilayer (XY).
> I would like to investigate the flux of ions (or other solutes like sugar) 
> that can pass through the protein.
> Unfortunately, I don't know the general rules to make a such simulation.
> 
> - Can I just add a higher concentration of ions in one side ? (if yes, should 
> I suppress PBC in Z axis ?)
> - Do I put the counter ions on the same side ?
> - So, do I have to make PBC condition only on XY plan ?
> - Is there an external electrical field to apply ? If yes, how ?
> 
> If you have general tutorial documentation, I would be happy to take a look 
> at it !
> 
> Thank you !
> Kind regards,
> Maximilien Lopes Rodrigues
> 
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Re: [gmx-users] simulation_time[Nikita Bora]

[Mark Abraham]

Hi,

A report written by the people who designed the method that describes how
they used it *is* a direct way to know the values to use. People they often
publish with are also probably pretty reliable. Even better still are the
people who show why their parameter choices work. The models didn't arrive
by divine inspiration :-)

Mark

On Thu, May 26, 2016 at 8:42 AM SAPNA BORAH  wrote:

> hi...
> So there is no direct way to know the values to be used .
> however the last line is still unclear...
>
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
>
> On Fri, May 20, 2016 at 12:00 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hi Nikita,
> >
> > It's not like there's a range to take a minimum from. It's this with this
> > force field and that with another. Any deviation will alter the behaviour
> > of the force field, and you'll have to show that the result is valid,
> > either by running tests, or by referring to a paper that has results from
> > such tests. The most suitable value is probably the one used by groups
> that
> > have direct ties to the developing group(s).
> >
> >
> > Hope it helps,
> >
> >
> > Tsjerk
> >
> >
> >
> > On May 20, 2016 07:20, "Ms. Nikita Bora"  wrote:
> >
> > > Thanks Tsjerk
> > >
> > > That was really a good explanation. And it helped me out a lot.
> > > Still,I would like to know what are the standard values for these
> > > parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used.
> > >
> > > As earlier it was mentioned that with different force field different
> > > value is used so is there any link where i can get to know the minimum
> > cut
> > > off values for these parameters and which value should be used for
> which
> > > force field or condition
> > >
> > > thanks
> > > Nikita
> > >
> > >
> > >
> > >   Original Message
> > 
> > > > Subject: Re: simulation_time
> > > > From:"Ms. Nikita Bora" 
> > > > Date:Mon, May 16, 2016 9:42 am
> > > > To:  nik...@tezu.ernet.in
> > > >
> > >
> >
> --
> > > >
> > > > Respected Sir,
> > > >
> > > > Thanks for the reply. I would further like to know that according to
> > this
> > > > tutorial
> > > > (
> > >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> > > )
> > > > the rvdw=rcoulomb=1 is used for the protein while according to this
> > > > tutorial
> > > > (
> > >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> > > )
> > > > rvdw=rcoulomb=1.4 is used. why a different value for the simple
> protein
> > > > and protein-ligand complex is used??
> > > >
> > >
> > > Different force fields, different settings.
> > >
> > > -Justin
> > >
> > > >
> > >
> > >
> > > ___
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Re: [gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD

[Mark Abraham]

Hi,

The number 1000 is suspiciously like a force constant someone would use for
position restraints, but somehow misnamed. Clearly the problem is external
to the fragment you shared, however.

Mark

On Thu, May 26, 2016 at 2:58 AM Justin Lemkul  wrote:

>
>
> On 5/25/16 9:21 AM, Wang Tao wrote:
> > Hi,Dr Justin!
> >
> > You have mentioned that i missed my itp file.Here is it
> > ##
> > 
> > [ moleculetype ]
> > ;molnamenrexcl
> >  OHIN  1
> >
> > [ atoms ]
> > ;id  at type  res nr  residue name at name cg nr charge mass
> > 1opls_434 1OHIN   OH  1   -1.300  15.999
> > 2opls_435 1OHIN   HO  20.300  1.008
> >
> > [ bonds ]
> > ;i j funct lengthforce.c
> >  1 2  1 0.09450  462750.4;
> > ##
> > As you can see, that is how i defined the itp file of OH-.
> >
> > Those parameters can be found in oplsaa.ff/ffbonded.itp and
> oplsaa.ff/ffnonbonded.itp files.They have been provided in gromacs version
> 4.6.7.
> > Here are they:
> > ##
> > 
> > HOOH  10.09450   462750.4   ; SUG(OL) wlj mod 0.96-> 0.945
> > ##
> > 
> >  opls_434   OH   8  15.99940-1.300   A3.2e-01
> 1.04600e+00
> >  opls_435   HO   1   1.00800 0.300   A0.0e+00
> 0.0e+00
> > ##
> > But i really don't understand why the bond in OH- is invalid.Or in
> another word,what can i do to finish an sucessful energy minimization with
> OH- in my system?
> >
>
> No idea; it works for me.  I built a system of one OH- in vacuo, applied
> your
> topology, and it worked fine.  Probably something in the .top is broken,
> and
> #include statement in the wrong place or something else.
>
> -Justin
>
> > You also said that waht i am conduncting is not a true constant PH
> MD.Yes,you are right.I did have some misunderstanding about it. But in my
> system ,i intended to create an environment where there is plenty of
> OH-with fixed concentration of it.So fixed protonation  is ok in this work.
> But anyway, i am very interested in constant-PH MD,and want to do something
> about it.I would spend more time on it.
> >
> > Now,would you please offer me some advice on solve my problem above?
> >
> > Tao Wang
> >
> > Thank You!
> >
> >
> > Message: 2
> > Date: Wed, 25 May 2016 07:04:59 -0400
> > From: Justin Lemkul 
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] gromacs energy minimization fatal error:
> > Invalid bond type 1000 in constant-PH MD
> > Message-ID: 
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 5/25/16 6:06 AM, Wang Tao wrote:
> >> Hi,every one!
> >>
> >> I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH
> is equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp
> file for OH- is created by myself.
> >>
> >
> > This is not what constant pH MD is.  You've got a fixed protonation
> state with
> > OH- floating around, which may not be physically realistic.
> >
> >> After having finished the genbox and genion steps sucessfully, i met a
> problem in energy minimization step. The output information says:Invalid
> bond type 1000. But i don't really understand what the exact problem is.
> >>
> >>
> >> Tried to remove bond definition in itp file for OH-, don't work.
> >>
> >> Tried to remove bond definition in ffbonded.itp for OH-, don't work.
> >>
> >> Replaced OH- with CL-,error infomation disappeared.
> >>
> >>
> >> I believe the problem is related to OH- force field parameters,but
> don't know how to deal with it.
> >>
> >
> > You haven't provided us with its topology, so there's nothing anyone can
> do but
> > guess haphazardly.  But if removing it solves the problem, you know
> exactly
> > where the issue is.
> >
> > -Justin
> >
> >>
> >> Can anyone help me?
> >>
> >>
> >> Tao Wang
> >>
> >> Thank You!
> >>
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > 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 629
> 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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> * Please search the archive at
> 

Re: [gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

[Mark Abraham]

Hi,

You need to build an MPI-enabled version of GROMACS, which will default to
being named gmx_mpi. Thus

/home/lipi/openmpi164/bin/mpirun -np 16
/app/setups/gromacs-5.1.1/build/bin/gmx_mpi mdrun -deffnm
step6.2_equilibration -rdd 1.8

Your run is starting 16 serial mdrun, which are then fighting over the same
checkpoint file.

Mark

On Thu, May 26, 2016 at 9:32 AM Antara mazumdar 
wrote:

> Dear Users,
>   I was trying to do equilibration of a mixed lipid vesicle using gromacs
> 5.1 in parallel using the below pasted pbs script :
>
>
> #!/bin/tcsh
> #PBS -l walltime=48:00:00
> #PBS -N VES_new_16
> #PBS -q workq
> #PBS -l select=1:ncpus=16:mpiprocs=16
> #PBS -V
>
> # Go to the directory from which you submitted the job
> cd $PBS_O_WORKDIR
>
> #export MPI_DEBUG=all
> #export MPI_IB_RAILS=2
> #export MPI_DSM_DISTRIBUTE=1
> #export MPI_VERBOSE=1
> #export MPI_BUFS_THRESHOLD=1
> #export MPI_BUFS_PER_PROC=1024
> #export OMP_NUM_THREADS=1
> #export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home1/gkpatra/gmp/lib
> module load intel-cluster-studio-2013
>
>
> setenv OMP_NUM_THREADS 1
> /home/lipi/openmpi164/bin/mpirun -np 16
> /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
> step6.2_equilibration -rdd 1.8 > test.dat
>
> This is generating multiple output and checkpoint files while its trying to
> run :
>
>
>  #step6.2_equilibration.xtc.6#
>  #step6.2_equilibration_step4400.cpt.1#
>  #step6.2_equilibration.log.3#
> #step6.2_equilibration.log.5#
>  #step6.2_equilibration.log.4#
>  #step6.2_equilibration.log.2#
>  step6.2_equilibration_prev.cpt
>  #step6.2_equilibration.log.6#
> step6.2_equilibration.cpt
> #step6.2_equilibration.xtc.3#
>  #step6.2_equilibration.xtc.5#
> #step6.2_equilibration.xtc.7#
> step6.2_equilibration.xtc
>
> When i check the log file to see the errors , it is showing the following :
>
>   Step   Time Lambda
>   00.00.0
>
>Energies (kJ/mol)
>Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
> 1.18159e+053.78079e+04   -8.79894e+06   -1.10782e+064.70754e+05
> Flat-bottom posres  PotentialKinetic En.   Total Energy
> Temperature
> 4.65013e+06   -4.62990e+062.25820e+02   -4.62968e+066.73923e-02
>  Pressure (bar)
>-7.74545e+01
>
> DD  step 39 load imb.: force 22.2%
>
> Writing checkpoint, step 560 at Thu May 26 11:57:56 2016
>
>
>
> ---
> Program gmx mdrun, VERSION 5.1.1
> Source code file:
> /app/setups/gromacs-5.1.1/src/gromacs/gmxlib/checkpoint.cpp, line: 1670
>
> File input/output error:
> Cannot rename checkpoint file; maybe you are out of disk space?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> I am not able to find the solution for it. What could be causing this? I
> have not been able to find help from HPC support available to us.
>
>
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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[gmx-users] Ion flux through membrane protein

[Maximilien LOPES RODRIGUES]

Dear GROMACS users,

first of all, thank you for paying attention to my question.

I have a system containing a membrane protein (porin) that is embedded in a 
lipid bilayer (XY).
I would like to investigate the flux of ions (or other solutes like sugar) that 
can pass through the protein.
Unfortunately, I don't know the general rules to make a such simulation.

- Can I just add a higher concentration of ions in one side ? (if yes, should I 
suppress PBC in Z axis ?)
- Do I put the counter ions on the same side ?
- So, do I have to make PBC condition only on XY plan ?
- Is there an external electrical field to apply ? If yes, how ?

If you have general tutorial documentation, I would be happy to take a look at 
it !

Thank you !
Kind regards,
Maximilien Lopes Rodrigues

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[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

[Antara mazumdar]

Dear Users,
  I was trying to do equilibration of a mixed lipid vesicle using gromacs
5.1 in parallel using the below pasted pbs script :


#!/bin/tcsh
#PBS -l walltime=48:00:00
#PBS -N VES_new_16
#PBS -q workq
#PBS -l select=1:ncpus=16:mpiprocs=16
#PBS -V

# Go to the directory from which you submitted the job
cd $PBS_O_WORKDIR

#export MPI_DEBUG=all
#export MPI_IB_RAILS=2
#export MPI_DSM_DISTRIBUTE=1
#export MPI_VERBOSE=1
#export MPI_BUFS_THRESHOLD=1
#export MPI_BUFS_PER_PROC=1024
#export OMP_NUM_THREADS=1
#export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home1/gkpatra/gmp/lib
module load intel-cluster-studio-2013


setenv OMP_NUM_THREADS 1
/home/lipi/openmpi164/bin/mpirun -np 16
/app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
step6.2_equilibration -rdd 1.8 > test.dat

This is generating multiple output and checkpoint files while its trying to
run :


 #step6.2_equilibration.xtc.6#
 #step6.2_equilibration_step4400.cpt.1#
 #step6.2_equilibration.log.3#
#step6.2_equilibration.log.5#
 #step6.2_equilibration.log.4#
 #step6.2_equilibration.log.2#
 step6.2_equilibration_prev.cpt
 #step6.2_equilibration.log.6#
step6.2_equilibration.cpt
#step6.2_equilibration.xtc.3#
 #step6.2_equilibration.xtc.5#
#step6.2_equilibration.xtc.7#
step6.2_equilibration.xtc

When i check the log file to see the errors , it is showing the following :

  Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
1.18159e+053.78079e+04   -8.79894e+06   -1.10782e+064.70754e+05
Flat-bottom posres  PotentialKinetic En.   Total Energy
Temperature
4.65013e+06   -4.62990e+062.25820e+02   -4.62968e+066.73923e-02
 Pressure (bar)
   -7.74545e+01

DD  step 39 load imb.: force 22.2%

Writing checkpoint, step 560 at Thu May 26 11:57:56 2016



---
Program gmx mdrun, VERSION 5.1.1
Source code file:
/app/setups/gromacs-5.1.1/src/gromacs/gmxlib/checkpoint.cpp, line: 1670

File input/output error:
Cannot rename checkpoint file; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



I am not able to find the solution for it. What could be causing this? I
have not been able to find help from HPC support available to us.



Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
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Re: [gmx-users] simulation_time[Nikita Bora]

[SAPNA BORAH]

hi...
So there is no direct way to know the values to be used .
however the last line is still unclear...


Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Fri, May 20, 2016 at 12:00 PM, Tsjerk Wassenaar 
wrote:

> Hi Nikita,
>
> It's not like there's a range to take a minimum from. It's this with this
> force field and that with another. Any deviation will alter the behaviour
> of the force field, and you'll have to show that the result is valid,
> either by running tests, or by referring to a paper that has results from
> such tests. The most suitable value is probably the one used by groups that
> have direct ties to the developing group(s).
>
>
> Hope it helps,
>
>
> Tsjerk
>
>
>
> On May 20, 2016 07:20, "Ms. Nikita Bora"  wrote:
>
> > Thanks Tsjerk
> >
> > That was really a good explanation. And it helped me out a lot.
> > Still,I would like to know what are the standard values for these
> > parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used.
> >
> > As earlier it was mentioned that with different force field different
> > value is used so is there any link where i can get to know the minimum
> cut
> > off values for these parameters and which value should be used for which
> > force field or condition
> >
> > thanks
> > Nikita
> >
> >
> >
> >   Original Message
> 
> > > Subject: Re: simulation_time
> > > From:"Ms. Nikita Bora" 
> > > Date:Mon, May 16, 2016 9:42 am
> > > To:  nik...@tezu.ernet.in
> > >
> >
> --
> > >
> > > Respected Sir,
> > >
> > > Thanks for the reply. I would further like to know that according to
> this
> > > tutorial
> > > (
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> > )
> > > the rvdw=rcoulomb=1 is used for the protein while according to this
> > > tutorial
> > > (
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> > )
> > > rvdw=rcoulomb=1.4 is used. why a different value for the simple protein
> > > and protein-ligand complex is used??
> > >
> >
> > Different force fields, different settings.
> >
> > -Justin
> >
> > >
> >
> >
> > ___
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