[gmx-users] Questions about the MFFA boundery implementation of Gromacs?

[song.yongshun]

 Dear all:
I was using the MFFA version of Gromacs which is provided by m.j.louhivuori at 
http://md.chem.rug.nl/~mara/mffa.html.
I have some quesition about this version:

i.I saw the implementation of MFFA always with the flip-flop of lipid.Can I 
apply the flip-flop with this MFFA version of Gromacs ?
ii.I also saw the description of implementation of MFFA along only one 
direction.Is this available in this MFFA version of Gromacs?


Anyone who is familar with it help me.
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[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist

[Christopher Neale]

If the corrupted frame is at 1000 ps, and you can not get at the data after the 
corrupted frame by using:
trjconv -b 1100 , then I suspect that you don't have any good solution here, 
unless the developers put in
some type of magic number at the start of each frame that you could search for 
with a c program (perhaps
contact the developers of gmx_rescue for advice?)

A related question is how you ended up with a long .trr file that has 
corruption in the middle.
Did that corruption happen at runtime or later due to a filesystem problem? If 
it was a later filesystem 
problem, then you might look into backup solutions. If it happened at runtime, 
then it would be 
useful to figure out what happened because ideally gromacs would not forever 
append to corrupted files
since many of us don't look at information in the .trr files until very late in 
the analysis and an optional
0.1% loss in efficiency might be reasonable to ensure that this doesn't happen 
(at least our system admins 
would tell us so). For that, you'll probably need to provide details, including 
what version of gromacs you 
used. 

Chris.


-- original message --

I have some corrupted frames in different trajectories. gmxcheck with .trr 
trajectories gives extraordinary positions or velocities and with .xtc 
trajectories gives rise to the magic number error. I am aware of the program 
gmx_rescue kindly offered to us by its developers. However, this program can 
only work with .xtc files. It is possible to rescue .trr files when there is a 
maximum of one corrupted frame by checking the size of healthy frames, chopping 
the parts of the trajectory before and after, using e.g. programs head and tail 
with the corresponding integer multiples of one healthy frame in bytes and 
stitching them together. However, when there is two or more corrupted frames in 
different locations, although it is not hard to spot the exact locations, it is 
no longer possible to remove the problematic frames size-wise (or at least it 
is less likely to succeed than winning the lottery) , since the size of each 
corrupted frame is non-standard. Is there any corresponding software to 
gmx_rescue that can be used with .trr files? Is there any other recent program 
or any other way of coping with the problem? I did not post any details of my 
systems or the specific error messages I get because I believe my question is 
clear.

Thank you in advance!

Best,
Yiannis
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Re: [gmx-users] Gromos 54A8 forcefield

[Justin Lemkul]

On 4/26/13 3:58 PM, Rajat Desikan wrote:

Hi All,
I just read the paper pertaining to Gromos 54A8. I was wondering if the
force field files were available somewhere?



ATB is usually a good source for Gromos96 parameter sets:

http://compbio.biosci.uq.edu.au/atb/

The latest they have is 54A7, though.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] _gpu_id failed

[Justin Lemkul]

On 4/26/13 3:37 PM, Albert wrote:

Hello:

  I am going to run gromacs with command:

mpirun -np 4 mdrun_mpi -s em.tpr -c em.gro -v -g em.log -gpu_id #0, #2, #3, #4


but it failed with messages:

Program mdrun_mpi, VERSION 4.6.1
Source code file:
/home/albert/install/source/gromacs-4.6.1/src/gmxlib/statutil.c, line: 364

Fatal error:
Expected a string argument for option -gpu_id

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



The -gpu_id option needs a continuous string of identifiers (see examples on 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization). 
Anything separated by a space is interpreted as a new command-line argument.


What you want is -gpu_id 0234

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Gromos 54A8 forcefield

[Rajat Desikan]

Hi All,
I just read the paper pertaining to Gromos 54A8. I was wondering if the
force field files were available somewhere?

Thanks. 



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/Gromos-54A8-forcefield-tp5007713.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] _gpu_id failed

[Albert]

Hello:

 I am going to run gromacs with command:

mpirun -np 4 mdrun_mpi -s em.tpr -c em.gro -v -g em.log -gpu_id #0, #2, 
#3, #4



but it failed with messages:

Program mdrun_mpi, VERSION 4.6.1
Source code file: 
/home/albert/install/source/gromacs-4.6.1/src/gmxlib/statutil.c, line: 364


Fatal error:
Expected a string argument for option -gpu_id

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Jede der Scherben spiegelt das Licht" (Wir sind Helden)

Error on node 3, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 3 out of 4

gcq#330: "Jede der Scherben spiegelt das Licht" (Wir sind Helden)


gcq#330: "Jede der Scherben spiegelt das Licht" (Wir sind Helden)


gcq#330: "Jede der Scherben spiegelt das Licht" (Wir sind Helden)

--
mpirun has exited due to process rank 2 with PID 10440 on
node tesla exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).


thank you very much
Albert
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[gmx-users] GPU efficiency question

[Albert]

Dear:

 I've got two GTX690 in a a workstation and I found that when I run the 
md production with following two command:


mpirun -np 4 md_run_mpi

or

mpirun -np 2 md_run_mpi

the efficiency are the same. I notice that gromacs can detect 4 GPU 
(probably because GTX690 have two core..):


4 GPUs detected on host node4:
  #0: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
  #1: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
  #2: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible
  #3: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC:  no, stat: compatible


why the "-np 2" and "-np 4" are the same efficiency? shouldn't it be 
faster for "-np 4" ?


thank you very much

Albert

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Re: [gmx-users] compile error

[Albert]

IC.

it works very well now.

thanks a lot
Albert


On 04/26/2013 08:01 PM, Szilárd Páll wrote:

You got a warning at configure-time that the nvcc host compiler can't
be set because the mpi compiler wrapper are used. Because of this,
nvcc is using gcc to compile CPU code whick chokes on the icc flags.
You can:
- set CUDA_HOST_COMPILER to the mpicc backend, i.e. icc or
- let cmake detect MPI and use simply CC=icc CXX=icpc cmake
-DGMX_MPI=ON (in this case the normal compiler are used and*if*  cmake
can detect the MPI libs it will not need the wrappers).

Cheers,
--
Szilárd


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Re: [gmx-users] compile error

[Szilárd Páll]

You got a warning at configure-time that the nvcc host compiler can't
be set because the mpi compiler wrapper are used. Because of this,
nvcc is using gcc to compile CPU code whick chokes on the icc flags.
You can:
- set CUDA_HOST_COMPILER to the mpicc backend, i.e. icc or
- let cmake detect MPI and use simply CC=icc CXX=icpc cmake
-DGMX_MPI=ON (in this case the normal compiler are used and *if* cmake
can detect the MPI libs it will not need the wrappers).

Cheers,
--
Szilárd


On Fri, Apr 26, 2013 at 6:45 PM, Albert  wrote:
> Dear:
>
>  I've installed gromacs-4.6.1 in a GPU workstation with two GTX690. Here is
> my step:
>
>
>
> ./configure --prefix=/home/albert/install/openmpi-1.4.5 CC=icc CXX=icpc
> F77=ifort FC=ifort
> make
> make install
>
>
> cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF
> -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-5.0
> -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1
> -DCMAKE_PREFIX_PATH=/opt/intel/mkl/include/fftw
> -DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpiCC
> -DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpicc
>
>
> however, it failed with messages:
>
> [  1%] Building NVCC (Device) object
> src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
> cc1plus: error: unrecognized command line option ‘-ip’
> CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message):
>   Error generating
> /home/albert/install/source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
>
>
> make[2]: ***
> [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o]
> Error 1
> make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
> make: *** [all] Error 2
>
>
> when I try to run make
>
> thank you very much
> best
> Albert
>
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[gmx-users] compile error

[Albert]

Dear:

 I've installed gromacs-4.6.1 in a GPU workstation with two GTX690. 
Here is my step:




./configure --prefix=/home/albert/install/openmpi-1.4.5 CC=icc CXX=icpc 
F77=ifort FC=ifort

make
make install


cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF 
-DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-5.0 
-DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1 
-DCMAKE_PREFIX_PATH=/opt/intel/mkl/include/fftw 
-DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpiCC 
-DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpicc



however, it failed with messages:

[  1%] Building NVCC (Device) object 
src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o

cc1plus: error: unrecognized command line option ‘-ip’
CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message):
  Error generating
/home/albert/install/source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o


make[2]: *** 
[src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] 
Error 1

make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
make: *** [all] Error 2


when I try to run make

thank you very much
best
Albert

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[gmx-users] Using virtual site

[라지브간디]

Dear gmx,


I am having a trouble in setting the virtual site on CO molecule. 


When I use V-site for CO, it end up with energy minimization error as follows:  




steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5
Step=0, Dmax= 1.0e-02 nm, Epot= -3.82767e+05 Fmax= 8.14332e+04, atom= 2512
Step=1, Dmax= 1.0e-02 nm, Epot= -3.90238e+05 Fmax= 8.68714e+04, atom= 2512
Step=2, Dmax= 1.2e-02 nm, Epot= -3.97776e+05 Fmax= 1.19106e+05, atom= 2512
Step=3, Dmax= 1.4e-02 nm, Epot= -4.06486e+05 Fmax= 2.90401e+05, atom= 2512
Step=4, Dmax= 1.7e-02 nm, Epot= -4.20168e+05 Fmax= 3.68606e+05, atom= 2512
Step=6, Dmax= 1.0e-02 nm, Epot= -4.22573e+05 Fmax= 3.77163e+05, atom= 2511
Step=8, Dmax= 6.2e-03 nm, Epot= -4.24217e+05 Fmax= 3.69075e+05, atom= 2512
Step=   10, Dmax= 3.7e-03 nm, Epot= -4.25217e+05 Fmax= 4.81625e+05, atom= 2511
Step=   12, Dmax= 2.2e-03 nm, Epot= -4.25618e+05 Fmax= 3.60189e+05, atom= 2512
Step=   13, Dmax= 2.7e-03 nm, Epot= -4.25861e+05 Fmax= 4.31397e+05, atom= 2511
Step=   15, Dmax= 1.6e-03 nm, Epot= -4.26278e+05 Fmax= 4.18024e+05, atom= 2512
Step=   17, Dmax= 9.7e-04 nm, Epot= -4.26642e+05 Fmax= 4.92899e+05, atom= 2511
Step=   19, Dmax= 5.8e-04 nm, Epot= -4.26741e+05 Fmax= 5.67952e+05, atom= 2512
Step=   21, Dmax= 3.5e-04 nm, Epot= -4.26911e+05 Fmax= 4.14681e+05, atom= 2511
Step=   23, Dmax= 2.1e-04 nm, Epot= -4.27011e+05 Fmax= 5.66533e+05, atom= 2512
Step=   25, Dmax= 1.3e-04 nm, Epot= -4.27043e+05 Fmax= 6.86227e+05, atom= 2511
Step=   27, Dmax= 7.5e-05 nm, Epot= -4.27086e+05 Fmax= 4.56863e+05, atom= 2512
Step=   29, Dmax= 4.5e-05 nm, Epot= -4.27110e+05 Fmax= 4.69971e+05, atom= 2511
Step=   31, Dmax= 2.7e-05 nm, Epot= -4.27126e+05 Fmax= 4.15923e+05, atom= 2512
Step=   32, Dmax= 3.2e-05 nm, Epot= -4.27135e+05 Fmax= 8.56354e+05, atom= 2511
Step=   34, Dmax= 1.9e-05 nm, Epot= -4.27146e+05 Fmax= 5.42283e+05, atom= 2512
Step=   36, Dmax= 1.2e-05 nm, Epot= -4.27152e+05 Fmax= 4.73218e+05, atom= 2511
Step=   37, Dmax= 1.4e-05 nm, Epot= -4.27155e+05 Fmax= 8.62092e+05, atom= 2512
Step=   39, Dmax= 8.4e-06 nm, Epot= -4.27162e+05 Fmax= 4.13479e+05, atom= 2511
Step=   40, Dmax= 1.0e-05 nm, Epot= -4.27164e+05 Fmax= 9.11108e+05, atom= 2512
Step=   42, Dmax= 6.1e-06 nm, Epot= -4.27168e+05 Fmax= 4.89792e+05, atom= 2511
Step=   44, Dmax= 3.6e-06 nm, Epot= -4.27170e+05 Fmax= 4.61416e+05, atom= 2512
Step=   45, Dmax= 4.4e-06 nm, Epot= -4.27171e+05 Fmax= 6.69155e+05, atom= 2511
Step=   47, Dmax= 2.6e-06 nm, Epot= -4.27173e+05 Fmax= 3.68335e+05, atom= 2512
Step=   48, Dmax= 3.1e-06 nm, Epot= -4.27175e+05 Fmax= 4.89636e+05, atom= 2511
Step=   49, Dmax= 3.8e-06 nm, Epot= -4.27175e+05 Fmax= 1.02472e+06, atom= 2512
Step=   51, Dmax= 2.3e-06 nm, Epot= -4.27178e+05 Fmax= 3.60939e+05, atom= 2511
Step=   52, Dmax= 2.7e-06 nm, Epot= -4.27179e+05 Fmax= 5.39389e+05, atom= 2512
Step=   54, Dmax= 1.6e-06 nm, Epot= -4.27180e+05 Fmax= 5.76323e+05, atom= 2511
Step=   55, Dmax= 2.0e-06 nm, Epot= -4.27180e+05 Fmax= 9.58450e+05, atom= 2512
Step=   56, Dmax= 2.3e-06 nm, Epot= -4.27180e+05 Fmax= 1.08106e+06, atom= 2511
Step=   58, Dmax= 1.4e-06 nm, Epot= -4.27182e+05 Fmax= 3.79287e+05, atom= 2512
Step=   59, Dmax= 1.7e-06 nm, Epot= -4.27182e+05 Fmax= 7.55107e+05, atom= 2511
Step=   61, Dmax= 1.0e-06 nm, Epot= -4.27183e+05 Fmax= 4.83668e+05, atom= 2512
Step=   62, Dmax= 1.2e-06 nm, Epot= -4.27183e+05 Fmax= 8.92245e+05, atom= 2511
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000


Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)


writing lowest energy coordinates.


Steepest Descents converged to machine precision in 63 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -4.2718281e+05
Maximum force =  4.8366841e+05 on atom 2512
Norm of force =  3.5896956e+03




BUT when i don't use V-site, it doesnt give any error as it runs without giving 
an any errors. I wonder I am making a problem in setting V-site ?


i run without using virtual site, its runs without any problem but if use 
virtual site for the ligand it gives this follwing error,


I assigned virtual site for CO ligand as like this : 


[ virtual_sites2 ]
; Vsite fromfunct   a
2513   2511   2512  1   0.4376625


Here, the 2511 is C, 2512 is O and 2513 the dummy (V-site) atom I given. I also 
manually included the V-site xyz coordinates value in .gro file.


What i am missing here?.


Please need an advice.














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Re: [gmx-users] Re: Manual installation of new analysis tool

[Venkat Reddy]

Dear Mark & Junghans,
I have got it. There is some problem in the Makefile. Thanks for your
suggestions and help


On Fri, Apr 26, 2013 at 11:12 AM, Venkat Reddy  wrote:

> Dear Mark & Junghans,
> Thanks for your valuable suggestions.
> I have gone through the README file. It says compatibility with 4.5.x
> version. I am using 4.5.5. So, I think its not a problem.
> @Junghans: I have installed pkg-config  in fact the $ pkg-config --libs
> libgmx returns
>the expected output; -lgmx -lm
>
> Here I am sending you the README file as attachment. Please go through it.
> If needed, I am happy to provide the code also.
>
> Thanks a lot
>
>
> On Fri, Apr 26, 2013 at 4:21 AM, Christoph Junghans wrote:
>
>> > Date: Thu, 25 Apr 2013 22:57:55 +0200
>> > From: Mark Abraham 
>> > Subject: Re: [gmx-users] Manual installation of new analysis tool
>> > To: Discussion list for GROMACS users 
>> > Message-ID:
>> > > 4wko947kc_y7s_gsyrxg8nms...@mail.gmail.com>
>> > Content-Type: text/plain; charset=ISO-8859-1
>> >
>> > On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy 
>> wrote:
>> >
>> >> Dear all,
>> >> I have got  an analysis tool for analyzing membrane density from
>> Dr.Luca
>> >> monticelli. I have followed the installation instructions as given.
>> >>
>> >> 1) First thing is to load GROMACS
>> >>$ *source /usr/local/gromacs/bin/GMXRC*
>> >> 2) Enter the source directory of the program then make
>> >>$ cd g_mydensity
>> >>$ make
>> >> According to the instructions, it should create an executable
>> >> "*g_mydensity*"
>> >> but I am getting the following errors
>> >>
>> >> *cc `pkg-config --libs libgmx`  g_mydensity.o matrix.o distances.o
>> >>
>> >
>> > Looks like his Makefile is relying on valid pkg-config registration.
>> I've
>> > no idea for what GROMACS versions under what conditions pkg-config
>> actually
>> > works, but I suggest you follow his instructions really precisely,
>> and/or
>> > contact him to resolve any doubtful points.
>> I added the pkg-config support with version 4.0.7 if I remember correctly.
>> Without knowing further details, two things come to my mind:
>> 0.) [Trivial] Make sure that pkg-config is actually installed.
>> 1.) Try if
>> $ pkg-config --libs libgmx
>> returns some useful output like "-lgmx -lm". If not, you might need to
>> set PKG_CONFIG_PATH to ${GMXLDLIB}/pkgconfig, but normally GMXRC does
>> that for you automatically.
>> 2.) Some functions in libgmx have been renamed/changed in the
>> development from 4.0 to 4.5 to 4.6, so you might actually need to
>> change the code, or use the same version as Dr.Luca Monticelli.
>>
>> Cheers,
>>
>> Christoph
>>
>>
>> >
>> > Mark
>> >
>> >
>> >> dist_mode.o grid_mode.o   -o g_mydensity*
>> >> *g_mydensity.o: In function `gmx_log2':*
>> >> *g_mydensity.c:(.text+0xa8): undefined reference to `log'*
>> >> *g_mydensity.o: In function `gmx_invsqrt':*
>> >> *g_mydensity.c:(.text+0xf2): undefined reference to
>> `gmx_invsqrt_exptab'*
>> >> *g_mydensity.c:(.text+0x101): undefined reference to
>> >> `gmx_invsqrt_fracttab'*
>> >> *g_mydensity.o: In function `matrix_convert':*
>> >> *g_mydensity.c:(.text+0x381): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x3ad): undefined reference to `sin'*
>> >> *g_mydensity.c:(.text+0x3da): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x403): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x416): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x429): undefined reference to `cos'*
>> >> *g_mydensity.c:(.text+0x447): undefined reference to `sin'*
>> >> *g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'*
>> >> *g_mydensity.o: In function `get_electrons':*
>> >> *g_mydensity.c:(.text+0x527): undefined reference to `ffopen'*
>> >> *g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'*
>> >> *g_mydensity.c:(.text+0x68d): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0x6eb): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0x74f): undefined reference to `ffclose'*
>> >> *g_mydensity.o: In function `center_coords':*
>> >> *g_mydensity.c:(.text+0x88f): undefined reference to `calc_box_center'*
>> >> *g_mydensity.o: In function `calc_electron_density':*
>> >> *g_mydensity.c:(.text+0x945): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0x973): undefined reference to `read_first_x'*
>> >> *g_mydensity.c:(.text+0x9a0): undefined reference to `gmx_fatal'*
>> >> *g_mydensity.c:(.text+0xa38): undefined reference to `save_calloc'*
>> >> *g_mydensity.c:(.text+0xa81): undefined reference to `save_calloc'*
>> >> *g_mydensity.c:(.text+0xac1): undefined reference to `save_calloc'*
>> >> *g_mydensity.c:(.text+0xaf6): undefined reference to `gmx_rmpbc_init'*
>> >> *g_mydensity.c:(.text+0xb

[gmx-users] Linear Interaction Energy Method (LIE)

[Rajitha Tatikonda]

Hi,

I am trying to calculate ligand binding affinity of Dimeric Protein(198
residues) complexed with a peptide(3 residues) using Linear Interaction
Energy method.The water box dimensions  of ligand  with protein and Ligand
in water are considered to be same.
I am  encountering problem in estimating long range electrostatic
interactions for ligand interacting with solvent. I have used PME for
coulomb-type (trajectory length  is 1ns)  The option I used in g_energy to
extract  long range electrostatic interactions is Coul-Recip and results
appear to be strange since,the electrostatic energy(EE for ligand in
solvent are more negative than electrostatic for ligand in protein, which
implies positive values for delta EE(quite weird!)
I just wanted to know what are the proper mdp options in order to get
meaningful results and also what is the option in g_energy to get LR
interactions, whether usage of Coul-Recip is correct or not? I also want to
know the cutoffs to be mentioned in order  to calculate SR and LR.
Whether I should be using Reaction Field or cut-off for treatment of LR
interactions
The mdp file which I have been using is attached below
title= Protein-Peptide Complex
; Run parameters
integrator= md; leap-frog integrator
nsteps= 50; 2 * 50 = 1000 ps, 1 ns
dt= 0.002; 2 fs
; Output control
nstxout= 1000; save coordinates every 2 ps
nstvout= 1000; save velocities every 2 ps
nstxtcout= 1000; xtc compressed trajectory output every 2 ps
nstenergy= 1000; save energies every 2 ps
nstlog= 1000; update log file every 2 ps
; Bond parameters
continuation= yes; Restarting after NPT
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 0.5; short-range neighborlist cutoff (in nm)
rcoulomb= 0.5; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein ; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t= 300 300; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
pbc= xyz; 3-D PBC
DispCorr= EnerPres; account for cut-off vdW scheme
gen_vel= no; Velocity generation is off

Many thanks in advance for your attention. I'd appreciate any help in this
regard.

Regards,
Hindu Tera
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Re: [gmx-users] mdrun on GPU

[Justin Lemkul]

On 4/26/13 10:50 AM, Juliette N. wrote:

Hi all,

I am going to use 4.6 version of gmx on GPU. I am not sure of the mdrun
command though. I used to use mpirun -np 4 mdrun_mpi -deffnm .. in 4.5.4.
Can I use the same command line as before for mdrun or other tools?



Please read through the documentation here first:

http://www.gromacs.org/Documentation/Acceleration_and_parallelization

The exact details depend on the configuration of your hardware.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] ATP/Mg+2 parameters

[George Patargias]

Hello

Doe anybody know what is the "best" (the most suitable) set of parameters
to use for ATP/Mg+2 ?

I have seen from the literature that people have used mainly either the
CHARMM27 parameters or the ones in

Meagher KL, Redman LT, Carlson HA (2003) Development of polyphosphate
parameters for use with the AMBER force field. J Comput Chem 24:1016

I would appreciate if you can give me any hints on this.

Thanks.


Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568

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[gmx-users] mdrun on GPU

[Juliette N.]

Hi all,

I am going to use 4.6 version of gmx on GPU. I am not sure of the mdrun
command though. I used to use mpirun -np 4 mdrun_mpi -deffnm .. in 4.5.4.
Can I use the same command line as before for mdrun or other tools?

Thank you very much,
-- 
J.
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Re: [gmx-users] Re: SMD - reproducibility

[André Farias de Moura]

there should be an extra option in your mdrun command line if
reproducibility is an issue:

-[no]reprod  bool   no  Try to avoid optimizations that affect binary
reproducibility

the value of -reprod is set to no by default, turn on that option and
trajectories should be the same.

best

Andre

On Fri, Apr 26, 2013 at 9:25 AM, Steven Neumann wrote:

> Thanks anyway. I will try tu pull it 20-40 times to tell something.
>
> Steven
>
> On Fri, Apr 26, 2013 at 1:23 PM, Thomas Schlesier  >wrote:
>
> > Don't know. One idea i have: Take a flexible and a relative rigid system
> > and perform simulations with the same starting conditions (-> using -t
> > *.cpt). I would imagine that for the flexible system the trajectories
> start
> > earlier to deviate, since more stuff could happen (system is more
> flexible
> > -> greater configurational space). For the rigid system the
> configurational
> > space is smaller, so the probability is higher to always follow the same
> > trajectory if one starts with a predefinded velocity and direction.
> > But don't know if this is true, but it's the first thing which comes to
> my
> > mind.
> >
> >
> > Am 26.04.2013 14:01, schrieb gmx-users-requ...@gromacs.org:
> >
> > Thanks for this. I think option 2 is more reasonable. However, still do
> not
> >> know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
> >> simulations...
> >>
> >> On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier **
> >> >wrote:
> >>
> >> >Think i now understand your question. Forget what i wrote before.
> >>> >I could imagine the the 'grompp -t npt.cpt' part is a problem.
> >>> >If the simulations would be numerical reproducible, one should get the
> >>> >same results. As they are not, the results will differ somewhat (would
> >>> >think the more, the longer you simulate). But two different
> simulations
> >>> >would be more equal to each other, than two simulations which start
> with
> >>> >different velocity distributions for the particles.
> >>> >
> >>> >
> >>> >If you're interested in an stochastic analysis of your system (meaning
> >>> >simulations which are not equal - performing many pulling experiments
> in
> >>> >reality, one would also have many different starting points) you could
> >>> do
> >>> >two things:
> >>> >1) Run a look npt simulation, and use different frames to start the
> SMD
> >>> >simulations. From each frame the particles should have a different
> >>> velocity
> >>> >distribution and the results of the SMD simulations should also
> differ.
> >>> >(Depending on how many SMD simulations you want to perform, this might
> >>> get
> >>> >expensive, since the starting frame for SMD should be separated by
> more
> >>> >then a few ps.)
> >>> >2) Dump the 'npt.cpt' file and randomly determine new velocities for
> >>> each
> >>> >particle at the start of each SMD simulation. Since each simulation
> has
> >>> a
> >>> >different velocity distribution, the SMD simulation wont be the same.
> >>> This
> >>> >approach has only one weak point. Due to assigning new random
> velocities
> >>> >you destroy the thermal equilibrium of the system. But if the system
> was
> >>> >well equilibrated before, this distrubance should only be small and
> >>> after
> >>> >the first 100-200 ps of the SMD simulaton the system is in thermal
> >>> >equilibrium. If the complete SMD simulation is much longer (couple of
> >>> ns),
> >>> >the interesting stuff would happen longer after the inital simulation
> >>> time
> >>> >with the destroyed equilibrium.
> >>> >
> >>> >Hope this helps
> >>> >Thomas
> >>> >
> >>> >
> >>> >
> >>> >Am 26.04.2013 12:00, schriebgmx-users-request@**gromacs.org<
> schriebgmx-users-requ...@gromacs.org>
> >>> :
> >>> >
> >>> >Dear Users,
> >>>
>  >>
>  >>I am running my puling simulations of ligand with constant velocity.
>  First
>  >>I minimize and equilibrate my system:
>  >>
>  >>grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
>  >>mdrun -s em.tpr -deffnm em
>  >>grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o
>  nvt298.tpr
>  >>mdrun -s nvt298.tpr -deffnm nvt298
>  >>grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
>  >>topol.top -o npt298.tpr
>  >>mdrun -s npt298.tpr -deffnm npt298
>  >>
>  >>Then I run 10 pulling simulations with the same mdp file:
>  >>
>  >>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t
>  npt298.cpt
>  >>-o
>  >>pull_1.tpr
>  >>mpiexec mdrun -s pull_1.tpr -deffnm pull_1
>  >>
>  >>...
>  >>
>  >>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t
>  npt298.cpt
>  >>-o
>  >>pull_10.tpr
>  >>mpiexec mdrun -s pull_10.tpr -deffnm pull_10
>  >>
>  >>
>  >>I get 3 different (but similar) profiles (Force vs time) with 10
>  >>simulations as some of them produce exactly the same results... In
>  another
>  >>system with the same methodology I get 10 si

Re: [gmx-users] Re: SMD - reproducibility

[rajendra kumar]

I am not sure but different force profiles may be due to the
non-equilibrium relaxation problem. The path on the energy landscape during
the non-equilibrium simulations depends on the pulling rate and/or
relaxation of any unknown coordinates correlated with pulling coordinates.
If during pulling, correlated coordinates will not be able to relax
completely, high energy path is more likely on the energy landscape. Effect
of relaxations can be tested by performing simulations at several reduced
pulling rate. Also, there are several literature available on the effect of
pulling rate during simulations.

With best regards,
Rajendra

On Fri, Apr 26, 2013 at 5:31 PM, Steven Neumann wrote:

> Thanks for this. I think option 2 is more reasonable. However, still do not
> know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
> simulations...
>
> On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier  >wrote:
>
> > Think i now understand your question. Forget what i wrote before.
> > I could imagine the the 'grompp -t npt.cpt' part is a problem.
> > If the simulations would be numerical reproducible, one should get the
> > same results. As they are not, the results will differ somewhat (would
> > think the more, the longer you simulate). But two different simulations
> > would be more equal to each other, than two simulations which start with
> > different velocity distributions for the particles.
> >
> >
> > If you're interested in an stochastic analysis of your system (meaning
> > simulations which are not equal - performing many pulling experiments in
> > reality, one would also have many different starting points) you could do
> > two things:
> > 1) Run a look npt simulation, and use different frames to start the SMD
> > simulations. From each frame the particles should have a different
> velocity
> > distribution and the results of the SMD simulations should also differ.
> > (Depending on how many SMD simulations you want to perform, this might
> get
> > expensive, since the starting frame for SMD should be separated by more
> > then a few ps.)
> > 2) Dump the 'npt.cpt' file and randomly determine new velocities for each
> > particle at the start of each SMD simulation. Since each simulation has a
> > different velocity distribution, the SMD simulation wont be the same.
> This
> > approach has only one weak point. Due to assigning new random velocities
> > you destroy the thermal equilibrium of the system. But if the system was
> > well equilibrated before, this distrubance should only be small and after
> > the first 100-200 ps of the SMD simulaton the system is in thermal
> > equilibrium. If the complete SMD simulation is much longer (couple of
> ns),
> > the interesting stuff would happen longer after the inital simulation
> time
> > with the destroyed equilibrium.
> >
> > Hope this helps
> > Thomas
> >
> >
> >
> > Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org:
> >
> > Dear Users,
> >>
> >> I am running my puling simulations of ligand with constant velocity.
> First
> >> I minimize and equilibrate my system:
> >>
> >> grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
> >> mdrun -s em.tpr -deffnm em
> >> grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
> >> mdrun -s nvt298.tpr -deffnm nvt298
> >> grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
> >> topol.top -o npt298.tpr
> >> mdrun -s npt298.tpr -deffnm npt298
> >>
> >> Then I run 10 pulling simulations with the same mdp file:
> >>
> >> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
> >> -o
> >> pull_1.tpr
> >> mpiexec mdrun -s pull_1.tpr -deffnm pull_1
> >>
> >> ...
> >>
> >> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
> >> -o
> >> pull_10.tpr
> >> mpiexec mdrun -s pull_10.tpr -deffnm pull_10
> >>
> >>
> >> I get 3 different (but similar) profiles (Force vs time) with 10
> >> simulations as some of them produce exactly the same results... In
> another
> >> system with the same methodology I get 10 similar but different
> profiles.
> >> I
> >> am wondering why in this case only 3 types are possible... Shall I try
> >> grompp without -t npt.cpt ?
> >>
> >> Steven
> >>
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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> >
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Re: [gmx-users] Issue with RMSD profile

[Justin Lemkul]

On 4/26/13 9:33 AM, Sainitin Donakonda wrote:

Hello all,

I ran 10ns molecular dynamics simulation of protein ligand complex ..in
which protein homology model..finally i analyzed .xtc file which is
produced after MD production run..first i plotted RMSD profile of backbone
of the protein ..it show that line starts from 0.2 nm to 0.4 nm and from it
is stabilized in plateau..

My question is  fluctuation in RMSD profile from 0.2nm to 0.4 nm is
acceptable range or not?

Can any body explain this



That sounds about reasonable for a normal, folded protein of average size, but 
do realize that a given value of RMSD basically tells you nothing.  More 
detailed assessment of the structure is required.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Issue with RMSD profile

[Sainitin Donakonda]

Hello all,

I ran 10ns molecular dynamics simulation of protein ligand complex ..in
which protein homology model..finally i analyzed .xtc file which is
produced after MD production run..first i plotted RMSD profile of backbone
of the protein ..it show that line starts from 0.2 nm to 0.4 nm and from it
is stabilized in plateau..

My question is  fluctuation in RMSD profile from 0.2nm to 0.4 nm is
acceptable range or not?

Can any body explain this

Thank you very much

Cheers,
Nitin
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[gmx-users] RE: Martini with PME, temp two low

[ABEL Stephane 175950]

Xavier, 

as i said in my message, this nstlist value is not optimal, but it works !!! if 
wlll try a higher nstlist value, if I have same problem in futur simulations 

Thanks again for you help 

Stephane




--

Message: 1
Date: Fri, 26 Apr 2013 07:58:12 +0200
From: XAvier Periole 
Subject: Re: [gmx-users] Re: Martini with PME,  temp two low (ABEL
Stephane 175950)
To: Discussion list for GROMACS users 
Message-ID: <6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl>
Content-Type: text/plain;   charset=us-ascii


Good. Note however that we do get the right temperature with a dt=20fs with 
Martini so you energy leak might be in the cutoff scheme or the system is 
really badly equilibrated.

On Apr 25, 2013, at 18:23, ABEL Stephane 175950  wrote:

> Xavier
>
> I have followed your suggestion and did a longer NPT equilibration with 
> smaller dt and ntlist values and It works. The Energy and Temp  reach to 
> stables values as i want.
>
> thank you again  for your help
>
> Stephane
>
> --
>
> Message: 2
> Date: Thu, 25 Apr 2013 14:17:00 +
> From: ABEL Stephane 175950 
> Subject: [gmx-users] Re: Martini with PME, temp two low
> To: "gmx-users@gromacs.org" 
> Message-ID:
><3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="us-ascii"
>
> @ Vitaly
> of course. I know that. My system is neutral  but with charged particles (AOT 
> and Na+).
>
> @Xavier
> I will try your suggestion and equilibrate my system for a longer period
>
> Thanks again
>
> Stephane
>
>
>
> --
>
> Message: 1
> Date: Thu, 25 Apr 2013 15:52:09 +0200
> From: XAvier Periole 
> Subject: Re: [gmx-users] Martini with PME, temp two low
> To: Discussion list for GROMACS users 
> Message-ID: <0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl>
> Content-Type: text/plain; charset=windows-1252
>
>
> Well ? 400 ps is rather small and you can expect deviations from so short 
> simulations if you start from an non-equilibrated system. I am not sure what 
> the void is but this indicates that your system might not be equilibrated ?
>
> You can try to decrease the time step and nstlist to see if you the drop of 
> temperature is due a flow of energy.
>
> On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950  
> wrote:
>
>> Hello Xavier,
>>
>> Thank you for your response.
>>
 nstlist = 10 and the rlist = 1.0
>> My mistake, i did not changes these values when i switched to PME,
>>
>> I have rerun the simulations for 400 ps in NPT with these changes and 
>> plotted Epot and Temp vs Time The Epot and Temp values are not stables. The 
>> average Temp of the system  is better than previously but fluctuate around 
>> (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations.
>>
>> I have also visualized my  system at the end of the NPT run, the  na+, 
>> water, surfactant, octane molecules  form a slab with void
>>
>> What's wrong ?
>>
>> Stephane
>>
>> --
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Re: [gmx-users] Re: SMD - reproducibility

[Steven Neumann]

Thanks anyway. I will try tu pull it 20-40 times to tell something.

Steven

On Fri, Apr 26, 2013 at 1:23 PM, Thomas Schlesier wrote:

> Don't know. One idea i have: Take a flexible and a relative rigid system
> and perform simulations with the same starting conditions (-> using -t
> *.cpt). I would imagine that for the flexible system the trajectories start
> earlier to deviate, since more stuff could happen (system is more flexible
> -> greater configurational space). For the rigid system the configurational
> space is smaller, so the probability is higher to always follow the same
> trajectory if one starts with a predefinded velocity and direction.
> But don't know if this is true, but it's the first thing which comes to my
> mind.
>
>
> Am 26.04.2013 14:01, schrieb gmx-users-requ...@gromacs.org:
>
> Thanks for this. I think option 2 is more reasonable. However, still do not
>> know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
>> simulations...
>>
>> On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier> >wrote:
>>
>> >Think i now understand your question. Forget what i wrote before.
>>> >I could imagine the the 'grompp -t npt.cpt' part is a problem.
>>> >If the simulations would be numerical reproducible, one should get the
>>> >same results. As they are not, the results will differ somewhat (would
>>> >think the more, the longer you simulate). But two different simulations
>>> >would be more equal to each other, than two simulations which start with
>>> >different velocity distributions for the particles.
>>> >
>>> >
>>> >If you're interested in an stochastic analysis of your system (meaning
>>> >simulations which are not equal - performing many pulling experiments in
>>> >reality, one would also have many different starting points) you could
>>> do
>>> >two things:
>>> >1) Run a look npt simulation, and use different frames to start the SMD
>>> >simulations. From each frame the particles should have a different
>>> velocity
>>> >distribution and the results of the SMD simulations should also differ.
>>> >(Depending on how many SMD simulations you want to perform, this might
>>> get
>>> >expensive, since the starting frame for SMD should be separated by more
>>> >then a few ps.)
>>> >2) Dump the 'npt.cpt' file and randomly determine new velocities for
>>> each
>>> >particle at the start of each SMD simulation. Since each simulation has
>>> a
>>> >different velocity distribution, the SMD simulation wont be the same.
>>> This
>>> >approach has only one weak point. Due to assigning new random velocities
>>> >you destroy the thermal equilibrium of the system. But if the system was
>>> >well equilibrated before, this distrubance should only be small and
>>> after
>>> >the first 100-200 ps of the SMD simulaton the system is in thermal
>>> >equilibrium. If the complete SMD simulation is much longer (couple of
>>> ns),
>>> >the interesting stuff would happen longer after the inital simulation
>>> time
>>> >with the destroyed equilibrium.
>>> >
>>> >Hope this helps
>>> >Thomas
>>> >
>>> >
>>> >
>>> >Am 26.04.2013 12:00, 
>>> >schriebgmx-users-request@**gromacs.org
>>> :
>>> >
>>> >Dear Users,
>>>
 >>
 >>I am running my puling simulations of ligand with constant velocity.
 First
 >>I minimize and equilibrate my system:
 >>
 >>grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
 >>mdrun -s em.tpr -deffnm em
 >>grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o
 nvt298.tpr
 >>mdrun -s nvt298.tpr -deffnm nvt298
 >>grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
 >>topol.top -o npt298.tpr
 >>mdrun -s npt298.tpr -deffnm npt298
 >>
 >>Then I run 10 pulling simulations with the same mdp file:
 >>
 >>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t
 npt298.cpt
 >>-o
 >>pull_1.tpr
 >>mpiexec mdrun -s pull_1.tpr -deffnm pull_1
 >>
 >>...
 >>
 >>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t
 npt298.cpt
 >>-o
 >>pull_10.tpr
 >>mpiexec mdrun -s pull_10.tpr -deffnm pull_10
 >>
 >>
 >>I get 3 different (but similar) profiles (Force vs time) with 10
 >>simulations as some of them produce exactly the same results... In
 another
 >>system with the same methodology I get 10 similar but different
 profiles.
 >>I
 >>am wondering why in this case only 3 types are possible... Shall I try
 >>grompp without -t npt.cpt ?
 >>
 >>Steven
 >>

>>>
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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[gmx-users] Re: SMD - reproducibility

[Thomas Schlesier]

Don't know. One idea i have: Take a flexible and a relative rigid system 
and perform simulations with the same starting conditions (-> using -t 
*.cpt). I would imagine that for the flexible system the trajectories 
start earlier to deviate, since more stuff could happen (system is more 
flexible -> greater configurational space). For the rigid system the 
configurational space is smaller, so the probability is higher to always 
follow the same trajectory if one starts with a predefinded velocity and 
direction.
But don't know if this is true, but it's the first thing which comes to 
my mind.



Am 26.04.2013 14:01, schrieb gmx-users-requ...@gromacs.org:

Thanks for this. I think option 2 is more reasonable. However, still do not
know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
simulations...

On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesierwrote:


>Think i now understand your question. Forget what i wrote before.
>I could imagine the the 'grompp -t npt.cpt' part is a problem.
>If the simulations would be numerical reproducible, one should get the
>same results. As they are not, the results will differ somewhat (would
>think the more, the longer you simulate). But two different simulations
>would be more equal to each other, than two simulations which start with
>different velocity distributions for the particles.
>
>
>If you're interested in an stochastic analysis of your system (meaning
>simulations which are not equal - performing many pulling experiments in
>reality, one would also have many different starting points) you could do
>two things:
>1) Run a look npt simulation, and use different frames to start the SMD
>simulations. From each frame the particles should have a different velocity
>distribution and the results of the SMD simulations should also differ.
>(Depending on how many SMD simulations you want to perform, this might get
>expensive, since the starting frame for SMD should be separated by more
>then a few ps.)
>2) Dump the 'npt.cpt' file and randomly determine new velocities for each
>particle at the start of each SMD simulation. Since each simulation has a
>different velocity distribution, the SMD simulation wont be the same. This
>approach has only one weak point. Due to assigning new random velocities
>you destroy the thermal equilibrium of the system. But if the system was
>well equilibrated before, this distrubance should only be small and after
>the first 100-200 ps of the SMD simulaton the system is in thermal
>equilibrium. If the complete SMD simulation is much longer (couple of ns),
>the interesting stuff would happen longer after the inital simulation time
>with the destroyed equilibrium.
>
>Hope this helps
>Thomas
>
>
>
>Am 26.04.2013 12:00, schriebgmx-users-requ...@gromacs.org:
>
>Dear Users,

>>
>>I am running my puling simulations of ligand with constant velocity. First
>>I minimize and equilibrate my system:
>>
>>grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
>>mdrun -s em.tpr -deffnm em
>>grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
>>mdrun -s nvt298.tpr -deffnm nvt298
>>grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
>>topol.top -o npt298.tpr
>>mdrun -s npt298.tpr -deffnm npt298
>>
>>Then I run 10 pulling simulations with the same mdp file:
>>
>>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
>>-o
>>pull_1.tpr
>>mpiexec mdrun -s pull_1.tpr -deffnm pull_1
>>
>>...
>>
>>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
>>-o
>>pull_10.tpr
>>mpiexec mdrun -s pull_10.tpr -deffnm pull_10
>>
>>
>>I get 3 different (but similar) profiles (Force vs time) with 10
>>simulations as some of them produce exactly the same results... In another
>>system with the same methodology I get 10 similar but different profiles.
>>I
>>am wondering why in this case only 3 types are possible... Shall I try
>>grompp without -t npt.cpt ?
>>
>>Steven
>>


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[gmx-users] Re: plots in gromacs

[vansh]

hey  thanks alot..got it :)




-
thanks in advance :)
--
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Re: [gmx-users] Re: SMD - reproducibility

[Steven Neumann]

Thanks for this. I think option 2 is more reasonable. However, still do not
know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
simulations...

On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier wrote:

> Think i now understand your question. Forget what i wrote before.
> I could imagine the the 'grompp -t npt.cpt' part is a problem.
> If the simulations would be numerical reproducible, one should get the
> same results. As they are not, the results will differ somewhat (would
> think the more, the longer you simulate). But two different simulations
> would be more equal to each other, than two simulations which start with
> different velocity distributions for the particles.
>
>
> If you're interested in an stochastic analysis of your system (meaning
> simulations which are not equal - performing many pulling experiments in
> reality, one would also have many different starting points) you could do
> two things:
> 1) Run a look npt simulation, and use different frames to start the SMD
> simulations. From each frame the particles should have a different velocity
> distribution and the results of the SMD simulations should also differ.
> (Depending on how many SMD simulations you want to perform, this might get
> expensive, since the starting frame for SMD should be separated by more
> then a few ps.)
> 2) Dump the 'npt.cpt' file and randomly determine new velocities for each
> particle at the start of each SMD simulation. Since each simulation has a
> different velocity distribution, the SMD simulation wont be the same. This
> approach has only one weak point. Due to assigning new random velocities
> you destroy the thermal equilibrium of the system. But if the system was
> well equilibrated before, this distrubance should only be small and after
> the first 100-200 ps of the SMD simulaton the system is in thermal
> equilibrium. If the complete SMD simulation is much longer (couple of ns),
> the interesting stuff would happen longer after the inital simulation time
> with the destroyed equilibrium.
>
> Hope this helps
> Thomas
>
>
>
> Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org:
>
> Dear Users,
>>
>> I am running my puling simulations of ligand with constant velocity. First
>> I minimize and equilibrate my system:
>>
>> grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
>> mdrun -s em.tpr -deffnm em
>> grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
>> mdrun -s nvt298.tpr -deffnm nvt298
>> grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
>> topol.top -o npt298.tpr
>> mdrun -s npt298.tpr -deffnm npt298
>>
>> Then I run 10 pulling simulations with the same mdp file:
>>
>> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
>> -o
>> pull_1.tpr
>> mpiexec mdrun -s pull_1.tpr -deffnm pull_1
>>
>> ...
>>
>> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
>> -o
>> pull_10.tpr
>> mpiexec mdrun -s pull_10.tpr -deffnm pull_10
>>
>>
>> I get 3 different (but similar) profiles (Force vs time) with 10
>> simulations as some of them produce exactly the same results... In another
>> system with the same methodology I get 10 similar but different profiles.
>> I
>> am wondering why in this case only 3 types are possible... Shall I try
>> grompp without -t npt.cpt ?
>>
>> Steven
>>
>
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
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> http://www.gromacs.org/**Support/Mailing_Lists
>
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[gmx-users] Re: SMD - reproducibility

[Thomas Schlesier]

Think i now understand your question. Forget what i wrote before.
I could imagine the the 'grompp -t npt.cpt' part is a problem.
If the simulations would be numerical reproducible, one should get the 
same results. As they are not, the results will differ somewhat (would 
think the more, the longer you simulate). But two different simulations 
would be more equal to each other, than two simulations which start with 
different velocity distributions for the particles.



If you're interested in an stochastic analysis of your system (meaning 
simulations which are not equal - performing many pulling experiments in 
reality, one would also have many different starting points) you could 
do two things:
1) Run a look npt simulation, and use different frames to start the SMD 
simulations. From each frame the particles should have a different 
velocity distribution and the results of the SMD simulations should also 
differ. (Depending on how many SMD simulations you want to perform, this 
might get expensive, since the starting frame for SMD should be 
separated by more then a few ps.)
2) Dump the 'npt.cpt' file and randomly determine new velocities for 
each particle at the start of each SMD simulation. Since each simulation 
has a different velocity distribution, the SMD simulation wont be the 
same. This approach has only one weak point. Due to assigning new random 
velocities you destroy the thermal equilibrium of the system. But if the 
system was well equilibrated before, this distrubance should only be 
small and after the first 100-200 ps of the SMD simulaton the system is 
in thermal equilibrium. If the complete SMD simulation is much longer 
(couple of ns), the interesting stuff would happen longer after the 
inital simulation time with the destroyed equilibrium.


Hope this helps
Thomas



Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org:

Dear Users,

I am running my puling simulations of ligand with constant velocity. First
I minimize and equilibrate my system:

grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
mdrun -s em.tpr -deffnm em
grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
mdrun -s nvt298.tpr -deffnm nvt298
grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
topol.top -o npt298.tpr
mdrun -s npt298.tpr -deffnm npt298

Then I run 10 pulling simulations with the same mdp file:

grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
pull_1.tpr
mpiexec mdrun -s pull_1.tpr -deffnm pull_1

...

grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
pull_10.tpr
mpiexec mdrun -s pull_10.tpr -deffnm pull_10


I get 3 different (but similar) profiles (Force vs time) with 10
simulations as some of them produce exactly the same results... In another
system with the same methodology I get 10 similar but different profiles. I
am wondering why in this case only 3 types are possible... Shall I try
grompp without -t npt.cpt ?

Steven


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Re: [gmx-users] xpm2ps issue

[Justin Lemkul]

On 4/26/13 4:33 AM, Neha Gandhi wrote:

Dear Gromacs Users and Developers,

I am doing do_dssp analyses using a trajectory and structure file both in
pdb format.
My trajectory is 1 microseconds (with snapshots saved every 10 ps), xpm2ps
doesn't show ticks on X-axis. I get following message:

Auto-tick spacing failed for X-axis, guessing 10009.

Upon do_dssp analyses only on 300 frames, ticks on both Y and X-axis are
visible. How can one play around with scales on X-axis? I tried tweaking
-bx and -size parameters but didn't help.


Any feedback is appreciated.



Specify spacing and other matrix properties using an .m2p file passed to the -di 
flag.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RE: Martini with PME, temp two low

[XAvier Periole]

nstlist of 2 is a be extreme! Did you try 5! It should be fine … but if your 
are happy that's ok :))

On Apr 26, 2013, at 12:37 PM, ABEL Stephane 175950  wrote:

> Hi Xavier, 
> 
> I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system 
> is stable and the energy well conserved (400 ns of run). I do know if it is 
> optimal but it works for my system. 
> 
> Stephane
> 
> 
> 
> --
> 
> Message: 1
> Date: Fri, 26 Apr 2013 07:58:12 +0200
> From: XAvier Periole 
> Subject: Re: [gmx-users] Re: Martini with PME,  temp two low (ABEL
>Stephane 175950)
> To: Discussion list for GROMACS users 
> Message-ID: <6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl>
> Content-Type: text/plain;   charset=us-ascii
> 
> 
> Good. Note however that we do get the right temperature with a dt=20fs with 
> Martini so you energy leak might be in the cutoff scheme or the system is 
> really badly equilibrated.
> 
> On Apr 25, 2013, at 18:23, ABEL Stephane 175950  wrote:
> 
>> Xavier
>> 
>> I have followed your suggestion and did a longer NPT equilibration with 
>> smaller dt and ntlist values and It works. The Energy and Temp  reach to 
>> stables values as i want.
>> 
>> thank you again  for your help
>> 
>> Stephane
>> 
>> --
>> 
>> Message: 2
>> Date: Thu, 25 Apr 2013 14:17:00 +
>> From: ABEL Stephane 175950 
>> Subject: [gmx-users] Re: Martini with PME, temp two low
>> To: "gmx-users@gromacs.org" 
>> Message-ID:
>>   <3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> @ Vitaly
>> of course. I know that. My system is neutral  but with charged particles 
>> (AOT and Na+).
>> 
>> @Xavier
>> I will try your suggestion and equilibrate my system for a longer period
>> 
>> Thanks again
>> 
>> Stephane
>> 
>> 
>> 
>> --
>> 
>> Message: 1
>> Date: Thu, 25 Apr 2013 15:52:09 +0200
>> From: XAvier Periole 
>> Subject: Re: [gmx-users] Martini with PME, temp two low
>> To: Discussion list for GROMACS users 
>> Message-ID: <0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl>
>> Content-Type: text/plain; charset=windows-1252
>> 
>> 
>> Well ? 400 ps is rather small and you can expect deviations from so short 
>> simulations if you start from an non-equilibrated system. I am not sure what 
>> the void is but this indicates that your system might not be equilibrated ?
>> 
>> You can try to decrease the time step and nstlist to see if you the drop of 
>> temperature is due a flow of energy.
>> 
>> On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950  
>> wrote:
>> 
>>> Hello Xavier,
>>> 
>>> Thank you for your response.
>>> 
> nstlist = 10 and the rlist = 1.0
>>> My mistake, i did not changes these values when i switched to PME,
>>> 
>>> I have rerun the simulations for 400 ps in NPT with these changes and 
>>> plotted Epot and Temp vs Time The Epot and Temp values are not stables. The 
>>> average Temp of the system  is better than previously but fluctuate around 
>>> (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations.
>>> 
>>> I have also visualized my  system at the end of the NPT run, the  na+, 
>>> water, surfactant, octane molecules  form a slab with void
>>> 
>>> What's wrong ?
>>> 
>>> Stephane
>>> 
>>> --
>> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Re: gmx-users Digest, Vol 108, Issue 165

[Thomas Schlesier]

TL;DR version (longer version below):
Due to the stochastic nature of SMD (and pulling experiments in general) 
it is quite natural that the results for different simulations will not 
be excatly the same.



I would say you are fine. Thing is, if you do ligand unbinding SMD 
simulations the unbinding process is a stochastic process and the 
results differ somewhat, most importantly the rupture force (highest 
force before the rupture event) will differ between the simulations and 
you'll get a distributions of rupture forces.


In a simple two-state model, the slope of force vs time, should be the 
same for each simulation before and after the rupture event (but 
probably different slopes before and after the rupture), only the time 
when the rupture event happens will change.
If your system is more complex (say a couple of bonds must be broken 
before the ligand unbinds), the slope before the rupture may vary 
between some simulations (in some simulations some of the bonds break 
earlier than in other simulatons.


In
http://pubs.acs.org/doi/full/10.1021/jp3115644
i looked into a system which can be described by a two-state model. The 
results from one typical trajectory are shown, but mostly i discuss the 
averaged results. If one compares the single trajectory and the 
averaged, one clearly sees that the trajectories varies around the 
rupture event, but at the start of the simulations the system behaves 
almost equal for each simulation.

Hope this helps.

Greetings
Thomas


Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org:

Dear Users,

I am running my puling simulations of ligand with constant velocity. First
I minimize and equilibrate my system:

grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
mdrun -s em.tpr -deffnm em
grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
mdrun -s nvt298.tpr -deffnm nvt298
grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
topol.top -o npt298.tpr
mdrun -s npt298.tpr -deffnm npt298

Then I run 10 pulling simulations with the same mdp file:

grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
pull_1.tpr
mpiexec mdrun -s pull_1.tpr -deffnm pull_1

...

grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
pull_10.tpr
mpiexec mdrun -s pull_10.tpr -deffnm pull_10


I get 3 different (but similar) profiles (Force vs time) with 10
simulations as some of them produce exactly the same results... In another
system with the same methodology I get 10 similar but different profiles. I
am wondering why in this case only 3 types are possible... Shall I try
grompp without -t npt.cpt ?

Steven


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[gmx-users] RE: Martini with PME, temp two low

[ABEL Stephane 175950]

Hi Xavier, 

I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system is 
stable and the energy well conserved (400 ns of run). I do know if it is 
optimal but it works for my system. 

Stephane



--

Message: 1
Date: Fri, 26 Apr 2013 07:58:12 +0200
From: XAvier Periole 
Subject: Re: [gmx-users] Re: Martini with PME,  temp two low (ABEL
Stephane 175950)
To: Discussion list for GROMACS users 
Message-ID: <6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl>
Content-Type: text/plain;   charset=us-ascii


Good. Note however that we do get the right temperature with a dt=20fs with 
Martini so you energy leak might be in the cutoff scheme or the system is 
really badly equilibrated.

On Apr 25, 2013, at 18:23, ABEL Stephane 175950  wrote:

> Xavier
>
> I have followed your suggestion and did a longer NPT equilibration with 
> smaller dt and ntlist values and It works. The Energy and Temp  reach to 
> stables values as i want.
>
> thank you again  for your help
>
> Stephane
>
> --
>
> Message: 2
> Date: Thu, 25 Apr 2013 14:17:00 +
> From: ABEL Stephane 175950 
> Subject: [gmx-users] Re: Martini with PME, temp two low
> To: "gmx-users@gromacs.org" 
> Message-ID:
><3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="us-ascii"
>
> @ Vitaly
> of course. I know that. My system is neutral  but with charged particles (AOT 
> and Na+).
>
> @Xavier
> I will try your suggestion and equilibrate my system for a longer period
>
> Thanks again
>
> Stephane
>
>
>
> --
>
> Message: 1
> Date: Thu, 25 Apr 2013 15:52:09 +0200
> From: XAvier Periole 
> Subject: Re: [gmx-users] Martini with PME, temp two low
> To: Discussion list for GROMACS users 
> Message-ID: <0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl>
> Content-Type: text/plain; charset=windows-1252
>
>
> Well ? 400 ps is rather small and you can expect deviations from so short 
> simulations if you start from an non-equilibrated system. I am not sure what 
> the void is but this indicates that your system might not be equilibrated ?
>
> You can try to decrease the time step and nstlist to see if you the drop of 
> temperature is due a flow of energy.
>
> On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950  
> wrote:
>
>> Hello Xavier,
>>
>> Thank you for your response.
>>
 nstlist = 10 and the rlist = 1.0
>> My mistake, i did not changes these values when i switched to PME,
>>
>> I have rerun the simulations for 400 ps in NPT with these changes and 
>> plotted Epot and Temp vs Time The Epot and Temp values are not stables. The 
>> average Temp of the system  is better than previously but fluctuate around 
>> (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations.
>>
>> I have also visualized my  system at the end of the NPT run, the  na+, 
>> water, surfactant, octane molecules  form a slab with void
>>
>> What's wrong ?
>>
>> Stephane
>>
>> --
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[gmx-users] SMD - reproducibility

[Steven Neumann]

Dear Users,

I am running my puling simulations of ligand with constant velocity. First
I minimize and equilibrate my system:

grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
mdrun -s em.tpr -deffnm em
grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
mdrun -s nvt298.tpr -deffnm nvt298
grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
topol.top -o npt298.tpr
mdrun -s npt298.tpr -deffnm npt298

Then I run 10 pulling simulations with the same mdp file:

grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
pull_1.tpr
mpiexec mdrun -s pull_1.tpr -deffnm pull_1

...

grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
pull_10.tpr
mpiexec mdrun -s pull_10.tpr -deffnm pull_10


I get 3 different (but similar) profiles (Force vs time) with 10
simulations as some of them produce exactly the same results... In another
system with the same methodology I get 10 similar but different profiles. I
am wondering why in this case only 3 types are possible... Shall I try
grompp without -t npt.cpt ?

Steven
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Re: [gmx-users] RMSD from the average structure

[bipin singh]

Dear Sir,

Thanks for the useful insight.


On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund  wrote:

> Average coordinates are problematic and not generally representative.
> Consider for instance the average coordinates of a methyl group connected
> to X. The rotation around the C-X bond causes the average positions of the
> hydrogens to line up. Consider using g_cluster to find representative
> structures from your trajectory.
>
> Erik
>
> On 26 Apr 2013, at 06:59, bipin singh  wrote:
>
> > Thanks for your reply.
> > Actually I am interested to see how much structural deviation is
> occurring
> > in a protein during the simulation from its average position of atoms
> > rather than the initial position (crystal structure or starting
> structure).
> > The motivation of doing this analysis is the fact that in real solution
> > phase, a system may not be static and if we consider the time average
> > structure of a simulation to be the real representative of the structure
> in
> > solution phase rather than static crystal structure.
> >
> >
> >
> >
> >
> >
> >
> > On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar 
> wrote:
> >
> >> Hi Bipin Singh,
> >>
> >> That indeed gives you the RMSD against the average. Do think about it a
> bit
> >> more: do you want the average of the whole structure, or should you
> account
> >> for a phase of relaxation?
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >>
> >> On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul  wrote:
> >>
> >>>
> >>>
> >>> On 4/24/13 3:06 AM, bipin singh wrote:
> >>>
>  Hi all,
> 
>  Please let me know whether this is the right way to calculate RMSD
> from
>  the
>  average structure from a simulation:
> 
>  g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
> 
> 
>  average.pdb: is the pdb file produced using -ox option of g_rmsf.
> 
> 
> >>> You can calculate RMSD with respect to whatever structure you like, but
> >>> the interpretation and justification for doing so are up to you.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==**==
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Research Scientist
> >>> Department of Biochemistry
> >>> Virginia Tech
> >>> Blacksburg, VA
> >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>>
> >>> ==**==
> >>>
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >>> * Please search the archive at http://www.gromacs.org/**
> >>> Support/Mailing_Lists/Search<
> >> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> >>> * Please don't post (un)subscribe requests to the list. Use the www
> >>> interface or send it to gmx-users-requ...@gromacs.org.
> >>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> >> http://www.gromacs.org/Support/Mailing_Lists>
> >>>
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >>
> >
> >
> >
> > --
> > *---
> > Thanks and Regards,
> > Bipin Singh*
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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-- 
*---
Thanks and Regards,
Bipin Singh*
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Re: [gmx-users] RMSD from the average structure

[Erik Marklund]

Average coordinates are problematic and not generally representative. Consider 
for instance the average coordinates of a methyl group connected to X. The 
rotation around the C-X bond causes the average positions of the hydrogens to 
line up. Consider using g_cluster to find representative structures from your 
trajectory.

Erik

On 26 Apr 2013, at 06:59, bipin singh  wrote:

> Thanks for your reply.
> Actually I am interested to see how much structural deviation is occurring
> in a protein during the simulation from its average position of atoms
> rather than the initial position (crystal structure or starting structure).
> The motivation of doing this analysis is the fact that in real solution
> phase, a system may not be static and if we consider the time average
> structure of a simulation to be the real representative of the structure in
> solution phase rather than static crystal structure.
> 
> 
> 
> 
> 
> 
> 
> On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar  wrote:
> 
>> Hi Bipin Singh,
>> 
>> That indeed gives you the RMSD against the average. Do think about it a bit
>> more: do you want the average of the whole structure, or should you account
>> for a phase of relaxation?
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> 
>> On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul  wrote:
>> 
>>> 
>>> 
>>> On 4/24/13 3:06 AM, bipin singh wrote:
>>> 
 Hi all,
 
 Please let me know whether this is the right way to calculate RMSD from
 the
 average structure from a simulation:
 
 g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
 
 
 average.pdb: is the pdb file produced using -ox option of g_rmsf.
 
 
>>> You can calculate RMSD with respect to whatever structure you like, but
>>> the interpretation and justification for doing so are up to you.
>>> 
>>> -Justin
>>> 
>>> --
>>> ==**==
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> 
>>> ==**==
>>> 
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<
>> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>> http://www.gromacs.org/Support/Mailing_Lists>
>>> 
>> 
>> 
>> 
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> 
> 
> 
> 
> -- 
> *---
> Thanks and Regards,
> Bipin Singh*
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Re: free energy of system

[sarah k]

Dear Justin,

Thanks for your response and the perfect tutorial. I found the details
I needed in it.

Best regards,
Sarah
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[gmx-users] xpm2ps issue

[Neha Gandhi]

Dear Gromacs Users and Developers,

I am doing do_dssp analyses using a trajectory and structure file both in
pdb format.
My trajectory is 1 microseconds (with snapshots saved every 10 ps), xpm2ps
doesn't show ticks on X-axis. I get following message:

Auto-tick spacing failed for X-axis, guessing 10009.

Upon do_dssp analyses only on 300 frames, ticks on both Y and X-axis are
visible. How can one play around with scales on X-axis? I tried tweaking
-bx and -size parameters but didn't help.


Any feedback is appreciated.

-- 
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
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[gmx-users] gmx 4.6.1, Expanded ensemble: weird balancing factors

[Joakim Jämbeck]

Dear Gromacs users,

I am trying to compute the free energy of hydration of ethane in order to get 
more familiar with the implementation of expanded ensemble in Gromacs v. 4.6.1.

The simulations runs fine and the balancing/weight factors are equilibrated 
after around 1.6 ns (a short equilibration time but this should be ok for a 
rough estimate of dG).

After this the simulation is continued for another 14 ns. At the end I look at 
the balancing factors to get a fast estimate of dG and see that they are tiny:

 MC-lambda information
  N  CoulL   VdwLCount   G(in kT)  dG(in kT)
  1  0.000  0.000162900.0   -0.09268
  2  0.200  0.00014940   -0.09268   -0.01647
  3  0.500  0.00014627   -0.10914   -0.03867 <<
  4  1.000  0.00014080   -0.147810.02986
  5  1.000  0.20014309   -0.117950.07408
  6  1.000  0.40015170   -0.043860.01711
  7  1.000  0.60015276   -0.02675   -0.02304
  8  1.000  0.80015061   -0.04979   -0.06110
  9  1.000  1.00014328   -0.110900.0

When adding these to get dG they value is way off what I get if I use the more 
traditional approach of separate simulations at each lambda value and using BAR 
at the end.

Does anyone have any ideas why I get these values?

Here is my mdp-file:

integrator = sd
tinit= 0
dt   = 0.001
nsteps  = 1500
comm-mode   = Linear
nstcomm = 10

nstlog   = 1000
nstenergy= 100
nstlist= 10
ns_type= grid
pbc= xyz
rlist = 1.0
cutoff-scheme  = verlet

coulombtype= PME
rcoulomb  = 1.0
vdw-type   = cutoff
rvdw   = 1.0
fourierspacing  = 0.12
pme_order= 4
ewald_rtol = 1e-04
DispCorr= EnerPres

tc-grps = System
tau_t= 5.0
ref_t = 300
Pcoupl= berendsen
tau_p   = 10.0
compressibility  = 4.5e-5
ref_p= 1.013
gen_vel   = no

constraints  = all-bonds
constraint-algorithm = lincs

; Free energy/expanded ensemble
free-energy= expanded
sc-alpha = 0.5
sc-r-power  = 6
init-lambda-state   = 0
coul-lambdas = 0.0 0.2 0.5 1.0 1.0 1.0 1.0 1.0 1.0
vdw-lambdas = 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0
calc-lambda-neighbors = 9
nstdhdl = 200
dhdl-print-energy   = yes
couple-moltype   = C1X
couple-lambda0  = vdw-q
couple-lambda1  = none
couple-intramol= no
nstexpanded = 100
lmc-stats= wang-landau
lmc-move   = metropolis
lmc-weights-equil = wl-delta
weight-equil-wl-delta = 0.001
wl-scale = 0.7
wl-ratio  = 0.8
init-wl-delta   = 1.0
wl-oneovert   = yes

Thanks in advance!

/ Joakim--
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Re: [gmx-users] issue in replica exchange

[Mark Abraham]

On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole  wrote:

>
> Thanks for the answer. I'll check gmx4.5.7 and report back.
>
> I am not sure what you mean by GROMACS swaps the coordinates not the
> ensemble data. The coupling to P and T and not exchanged with it?


The code in src/kernel/repl_ex.c:

static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc= state->ngtc * state->nhchainlength;
nnhpres = state->nnhpres* state->nhchainlength;
exchange_rvecs(ms, b, state->box, DIM);
exchange_rvecs(ms, b, state->box_rel, DIM);
exchange_rvecs(ms, b, state->boxv, DIM);
exchange_reals(ms, b, &(state->veta), 1);
exchange_reals(ms, b, &(state->vol0), 1);
exchange_rvecs(ms, b, state->svir_prev, DIM);
exchange_rvecs(ms, b, state->fvir_prev, DIM);
exchange_rvecs(ms, b, state->pres_prev, DIM);
exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
exchange_doubles(ms, b, state->therm_integral, state->ngtc);
exchange_rvecs(ms, b, state->x, state->natoms);
exchange_rvecs(ms, b, state->v, state->natoms);
exchange_rvecs(ms, b, state->sd_X, state->natoms);
}

I mis-stated last night - there *is* exchange of ensemble data, but it is
incomplete. In particular, state->ekinstate is not exchanged. Probably it
is incomplete because the 9-year-old comment about t_state changing is in a
location that nobody changing t_state will see. And serializing a complex C
data structure over MPI is tedious at best. But that is not really an
excuse for the non-modularity GROMACS has for many of its key data
structures. We are working on various workflow and actual code structure
improvements to fix/prevent issues like this, but the proliferation of
algorithms that ought to be inter-operable makes the job pretty hard.

Other codes seem to exchange the ensemble label data (e.g. reference
temperatures for T-coupling) because they write trajectories that are
continuous with respect to atomic coordinates. I plan to move REMD in
GROMACS to this approach, because it scales better, but it will not happen
any time soon.

That would explain what I see, but let see what 4.5.7 has to say first.
>

Great. It may be that there were other issues in 4.5.3 that exacerbated any
REMD problem.

Mark

Tks.
>
> On Apr 25, 2013, at 22:40, Mark Abraham  wrote:
>
> > Thanks for the good report. There have been some known issues about the
> > timing of coupling stages with respect to various intervals between
> GROMACS
> > events for some algorithms. There are a lot of fixed problems in 4.5.7
> that
> > are not specific to REMD, but I have a few lingering doubts about whether
> > we should be exchanging (scaled) coupling values along with the
> > coordinates. (Unlike most REMD implementations, GROMACS swaps the
> > coordinates, not the ensemble data.) If you can reproduce those kinds of
> > symptoms in 4.5.7 (whether or not they then crash) then there looks like
> > there may be a problem with the REMD implementation that is perhaps
> evident
> > only with the kind of large time step Martini takes?
> >
> > Mark
> >
> >
> > On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole 
> wrote:
> >
> >>
> >> Hi,
> >>
> >> I have been recently using the REMD code in gmx-407 and gmx-453 and got
> a
> >> few systems crashing for unclear reasons so far. The main tests I made
> are
> >> using gmx407 but it is all reproducible with gmx453. The crashing was
> also
> >> reproduced (not necessarily at the same time point) on several
> >> architectures.
> >>
> >> The system is made of a pair of proteins in a membrane patch and for
> which
> >> the relative orientation is controlled by non-native
> bond/angles/dihedrals
> >> to perform an umbrella sampling. I use the MARTINI force field but that
> >> might not be relevant here.
> >>
> >> The crashes occur following exchanges that do not seem to occur the
> >> correct way and preceded by pressure scaling warnings … indicative of a
> >> strong destabilisation of the system and eventual explosion. Some
> >> information seems to be exchanged inaccurately.
> >>
> >> Trying to nail down the problem I got stuck and may be some one can
> help.
> >> I placed a pdf file showing plots of bonded/nonbonded energies,
> >> temperatures, box size etc … around an exchange that does not lead to a
> >> crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff
> >> every step with the temperature colour coded as indicated in the first
> >> figure.
> >>
> >> From the figure it appears that the step right after the exchange there
> is
> >> a huge jump of Potential energy coming from the LJ(SR) part of it.
> Although
> >> there are some small discontinuities in the progression of the bond and
> >> angle energy around the