Re: [gmx-users] The time for the temperature and pressure coupling

[Erik Marklund]

Hi,

Perhaps a side point: Temperature and pressure can not be seen as  
constraints to the system at any given instant in the sense that e.g.  
the instantaneous kinetic energy perfectly match the temperature at  
every time step just because you have a thermostat. Time and ensemble  
averages will, however, reflect the temperature and pressure coupling.


Erik

On Feb 6, 2013, at 11:28 PM, Bao Kai wrote:


Dear Gromacs Team,

I have a small question related to the scheme of the MD in Gromacs.

When are the temperature and pressure constrains are enforced, before
the update of the velocity and position or after?

Thank you very much.

Best Regards,
Kai
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Re: [gmx-users] compiling on different architecture than the compute nodes architecture

[Broadbent, Richard]

Dear Silard,

cmake -DGMX_CPU_ACCELERATION=AVX_256 -DGMX_DEFAULT_SUFFIX=OFF
-DGMX_BINARY_SUFFIX="_avx"  -DGMX_OPENMP=ON  -DGMX_MPI=ON -DGMX_DOUBLE=ON
-DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR=$MKLROOT/include
-DMKL_LIBRARIES="$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/l
ibmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so"
-DCMAKE_INSTALL_PREFIX=$HOME/libs/gromacs

Compiled, linked and installed without warning using intel-suite/2013,
mpi/intel-3.1, and cmake/2.8.9 I was compiling release-4-6 out of the git
repository ( 06935659a3125d9b44b84c57e67cb6788fda42c1 ). The job using
that executable is still in the queue, however, another one built using
the sse2 kernels ran a minimisation on a single core without problems.

How much faster fftw3 is than mkl for gromacs, is the difference likely to
be on the scale of 1-2% or 10%?

Thanks,

Richard


On 07/02/2013 02:17, "Szilárd Páll"  wrote:

>On Wed, Feb 6, 2013 at 6:03 PM, Richard Broadbent <
>richard.broadben...@imperial.ac.uk> wrote:
>
>> Dear All,
>>
>> I would like to compile gromacs 4.6 to run with the correct acceleration
>> on the compute nodes on our local cluster. Some of the nodes have intel
>> sandy-bridge whilst others only have sse4.1 and some (including the
>>login
>> and single core job nodes) are still stuck on ssse3 (gmx would use sse2
>> acceleration here).
>>
>> Installing several versions is not a problem however, I'm not sure how
>>to
>> make cmake build a version of the code that is not using the
>>acceleration
>> for the system on which the code is being compiled. Restrictions on job
>> sizes makes running the compilation on the sandy-bridge nodes almost
>> impossible. Can anyone let me know which flags cmake needs to enable
>> avx-256 acceleration?
>>
>> my standard cmake line is:
>>
>> $ CC=mpiicc CXX=mpiicpc ; cmake -DGMX_OPENMP=ON  -DGMX_MPI=ON
>> -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON
>> -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/**include
>> -DMKL_LIBRARIES="$MKLROOT/lib/**intel64/libmkl_core.so;$**
>> 
>>MKLROOT/lib/intel64/libmkl_**intel_lp64.so;$MKLROOT/lib/**intel64/libmkl_
>>sequential.so"
>> -DCMAKE_INSTALL_PREFIX=$HOME/**libs/gromacs  ../
>>
>
>Note that MKL (without the fftw wrappers) is known to not work out of the
>box. Making it work requires a fairly simple workaround described here:
>http://redmine.gromacs.org/issues/1110#note-3
>
>Additionally, note that FFTW is in most cases faster than MKL (but if you
>find the contrary do let us know).
>
>--
>Szilárd
>
>
>
>>
>>
>>
>> Thanks,
>>
>> Richard
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Re: [gmx-users] RNA MD

[Erik Marklund]

I've never seen good parameters for nucleic acids. There might be  
such, but none that ship with gromacs as far as I know.


Erik

On Feb 7, 2013, at 4:25 AM, 김현식 wrote:


Dear experts,
Hello!
Is it possible to run RNA md with GBSA?


Thank you.
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[gmx-users] problems for GPU simulations

[Albert]

Hello:

 I got a workstation with two GTX590 which have two core for each GPU. 
I can submit gromacs GPU jobs with command:


mpirun  -np 4 mdrun .

with such running, I can get 26ns/day for Gromacs-4.6 beta version.

However, I found that for Gromacs-4.6 final version (which is the latest 
one), it claimed that I only have two GPU, it asked me to adjust -np to 2.


so I submit the jobs with command:

mpirun -np 2 mdrun...

for the same system with the same paramters (of course the tpr file must 
be regenerated). I found that I can get only half of the speed, 
something around 10 ns/day.



So I am just wondering what's happening?

thank you very much
best
Albert
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[gmx-users] Re: Error- Simulation box resizes during mdrun

[Bharath K. Srikanth]

Hi Justin:

Thanks for your reply. Yes, I did everything you mentioned. Let me explain
my steps in a bit more detail.

1) I had a lipid bilayer and a peptide from a previous simulation (in a
box 15 nm x 7.5 nm x 7.5 nm- 15 nm being perpendicular to the plane of the
bilayer). I removed the water and the peptides, so I had only the bilayer
left.

2) I then resized the box using editconf (the -box option) to a cubical
box of 7.5 nm in all directions. The bilayer remained in the center of the
new box.

3) I then re-inserted the peptide by editing the coordinate file, and ran
an energy minimization. Then I added water using genbox, and ran another
EM.

4) Then I ran the simulation for 3,000,000 steps (90 ns). While this was
happening, I observed that the size of the box was beginning to change, in
the z direction (not in the y direction as I said yesterday, but still,
parallel to the plane of the bilayer).

I've included some pictures here (in the .tga format), from before and
after the simulation. When I ran it in vmd using the initial coordinates
and the trajectory file, I could actually see the box resizing during the
run.

https://www.dropbox.com/l/UJuFbDTPaISIpkSf

I'm sure there's a very simple explanation, but I can't seem to figure it
out.

Thanks!

Regards,
Bharath

On 2/6/13 11:52 AM, Bharath K. Srikanth wrote:
> Hi everyone,
> Today, I was attempting a simulation of a system with a lipid bilayer,
and
> the size of my simulation box, obtained from a previous simulation, was
15
> nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the
plane
> of the bilayer). The bilayer consisted of 128 DOPC lipids and was
located
> at the centre of the box. I used periodic boundary conditions in all
three
> directions.
> I then resized the box to 7.5 nm in all directions, using the editconf
-box option. After doing the requisite energy minimization steps, I ran
the simulation using mdrun. However, running the simulation caused the
box
> to gradually shrink in the y-direction (parallel to the plane of the
bilayer!) during the simulation, ultimately settling at around half the
original dimension. Is there anything I may have done that could cause
this effect? I'm thoroughly baffled.

What do you mean by "resized the box?"  Did you strip out water, adjust box
vectors, re-solvate, equilibrate, etc?  What you're describing is very weird;
pictures, plots, etc would help a lot here.

-Justin




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Re: [gmx-users] system far from the equilibration state

[Shima Arasteh]

Thanks for your reply. 
How would I know that when I get close to the equilibration state?  By 
Pressure, Temperature,or  RMSD plots?


Thanks in advance for your suggestions.

Sincerely,
Shima



From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Monday, February 4, 2013 11:37 PM
Subject: Re: [gmx-users] system far from the equilibration state



On 2/4/13 2:04 PM, Shima Arasteh wrote:
> Hi,
>
> I am simulating a system of peptide/membrane/water. If my system is far from 
> the equilibration, would that be correct if I use Berendsen pressure coupling 
> for nano seconds to do NPT equilibration and then change it to 
> Parrinello-Rahman to get the true pressure? Anybody may suggest me please?
>

Sounds reasonable.  Berendsen is a useful method in such cases.

-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] problems for GPU simulations

[James Starlight]

Hi Albert!


As I understood your correctly you have run simulations with your 2
GPU cards on Gromacs-beta but could not do it with final version
havent it?

Could you tell me how you installed both GPU in your work-station?
Have you used SLI ? ( I've heard that gromacs is not suported the
simulation in multi-GPU regime so I'll be very happy if it's not true
:))

Also could you tell me about configuration of your workstation in more
detailes ? ( what cpu and mb you  use ? )


James

2013/2/7 Albert :
> Hello:
>
>  I got a workstation with two GTX590 which have two core for each GPU. I can
> submit gromacs GPU jobs with command:
>
> mpirun  -np 4 mdrun .
>
> with such running, I can get 26ns/day for Gromacs-4.6 beta version.
>
> However, I found that for Gromacs-4.6 final version (which is the latest
> one), it claimed that I only have two GPU, it asked me to adjust -np to 2.
>
> so I submit the jobs with command:
>
> mpirun -np 2 mdrun...
>
> for the same system with the same paramters (of course the tpr file must be
> regenerated). I found that I can get only half of the speed, something
> around 10 ns/day.
>
>
> So I am just wondering what's happening?
>
> thank you very much
> best
> Albert
> --
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Re: [gmx-users] Re: protein-ligand interactions in charmm force field

[James Starlight]

Justin,

Thanks again for suggestion. I've found that g_mindist is exactly what
I need. I'm not quite sure how I could use that tools to find all
possible interactions between my ligand and several polar residues
defined in the ndx file ( I have no problem only when I examined
manually each possible interaction separately). Finally I'm not quite
sure about number of contacts calculated by g_mindist. E.g I've
examined it for my ligand ( having 3 polar atoms and large hydrophobic
ring)  and 1 serine residue ( 1 polar side chain group ). As the
ouitput I've obtain 60 maximum contact number (and 10- minimum). Why
maximum number was so big ?

Some another question- I want to find a way to esstimate average
mobility of my ligands in the ligand binding pocket.
For example I have 2 different complexes of my protein with 2
different ligands- one of that liugand is big and occupy big spacy
whithin protein interiour ( so that ligand is less mobile). On the
contrary the second ligand is samller and flexible so it muast be more
mobile within protein and it seen visually during visualisation of the
md trajectory. But how it could be estimated in some values ?


Thanks for help

James

2013/2/7 Justin Lemkul :
>
>
> On 2/6/13 2:54 PM, James Starlight wrote:
>>
>> by the way could someone provide me with some simple tutorial of the
>> usage of the CGenFF for construction ITP topology for charmm f.f ?
>>
>>
>> Also I still could not found any simple way to monitor dynamics of the
>> non-covalent interactions between ligand and ligand binding pocket.
>> E.g I select manually in the ndx file all residues which could be
>> involved in such interactions (including formation of  possible
>> h.bonds, salt bridges as well as stacking interactions ) in one group
>> and ligand inthe second group. Should I use combination of g_hbond and
>> g_saltbr tools for such identification? How stacking interactions
>> could be monitored?
>>
>
> g_hbond, g_dist, and g_mindist -on with clever use of index groups can
> address all of these.
>
> -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] MARTINI force-field in pulling simulations

[Davide Mercadante]

Dear All,

I am trying to run a pulling simulation on a small protein (18 aa) using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions NA+ and CL-.

After the equilibration I start a constant velocity pulling along the
z-direction of the last atom of the chain while the first atom is
positionally restrained in xyz (basically I am stretching the protein).
At some point from the start of the pulling simulation and before
reaching the full extension of the chain (force profile is still
steadily increasing without peaking) the simulation crashes giving me
these LINCS warnings:

Step 293252, time 5865.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.157274, max 0.291135 (between atoms 10 and 11)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 293252, time 5865.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.128562, max 0.230219 (between atoms 7 and 8)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.413291, max 0.828515 (between atoms 7 and 8)

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.587032, max 0.986890 (between atoms 11 and 13)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  7  8   46.60.2686   0.0579  0.3500
 10 11  121.30.2481   0.0550  0.3500
 13 15  168.50.2851   0.0278  0.3500

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.108373, max 0.322423 (between atoms 19 and 21)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  7  8   45.00.2686   0.0600  0.3500
 10 11   88.10.2481   0.0497  0.3500
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.330732, max 0.654588 (between atoms 23 and 25)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 23   42.00.2905   0.1426  0.3500
 17 18   92.90.3146   0.1560  0.3000
 15 17   35.30.5839   0.4003  0.3500
 13 15  141.60.0278   0.2742  0.3500

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.312540, max 0.87 (between atoms 19 and 21)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  8  9   48.00.3406   0.1435  0.3100
  7  8   82.30.0579   0.4596  0.3500
 10 11  102.90.0550   0.5130  0.3500
 11 12   51.90.5425   0.3643  0.4000
 11 13   38.50.6954   0.1898  0.3500
 13 15  143.40.0278   0.2879  0.3500
 15 17   37.30.5839   0.3730  0.3500

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.343084, max 0.751867 (between atoms 3 and 5)
 17 18   93.20.3146   0.1563  0.3000
 21 23   41.60.2905   0.1443  0.3500
 23 24   33.00.3784   0.4007  0.4000
 11 13   58.20.6954   0.3283  0.3500
 23 24   33.10.3784   0.3999  0.4000
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  7  8   82.20.0579   0.4605  0.3500
  8  9   48.40.3406   0.1439  0.3100
 10 11  104.00.0550   0.5496  0.3500
 11 12   57.60.5425   0.3679  0.4000
 11 13   61.90.6954   0.1402  0.3500
 13 15  141.20.0278   0.4588  0.3500
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Step 293255, time 5865.1 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 32.745333, max 105.228383 (between atoms 17 and 18)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  5  6   30.30.3950   0.3971  0.4000
 13 15  172.90.2879   4.6287  0.3500
 15 16   33.00.2435   5.0674  0.3300
 15 17   51.20.3730  11.1793  0.3500
 17 18  107.10.1563  31.8685  0.3000
 17 19  143.40.3380  10.1576  0.3500
 19 20   86.50.3397   6.2047  0.3300
 21 22  103.70.3750   6.622

Re: [gmx-users] problems for GPU simulations

[Albert]

On 02/07/2013 11:03 AM, James Starlight wrote:

Hi Albert!


As I understood your correctly you have run simulations with your 2
GPU cards on Gromacs-beta but could not do it with final version
havent it?
not really. both versions could run with GPU. The 4.6 beta recognize my 
number of GPU as  4, but final version as 2. And the efficiency for beta 
is double comparing with final version.





Could you tell me how you installed both GPU in your work-station?
Have you used SLI ? ( I've heard that gromacs is not suported the
simulation in multi-GPU regime so I'll be very happy if it's not true
:))

both GPU version were compiled with the same command:

cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC 
-DCMAKE_C_COMPILER=/soft/openmpi-1.4.3/bin/mpicc 
-DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6beta3 -DGMX_GPU=OFF 
-DBUILD_SHARED_LIBS=OFF -DCMAKE_PREFIX_PATH=/soft/fftw-3.3.3


I don't think I used SLI



Also could you tell me about configuration of your workstation in more
detailes ? ( what cpu and mb you  use ? )
there are 16 GB for the memory,  I've got intel I7-960 for the 
workstation. I don't specify how many core should be used, but both 
cases occupy full CPU resources automatically.






James


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Re: [gmx-users] problems for GPU simulations

[James Starlight]

Albert,

thanks for information!

So now it's only intresting to my how I should install multi-GPU's on
my system to obtain best compatibility with gromacs.

Also could you tell me what your system has performance (in gflops)
and what system you have simulated on it (average atom number,
presence of explicit membrane etc)?


Thank you for help again,

James

2013/2/7 Albert :
> On 02/07/2013 11:03 AM, James Starlight wrote:
>>
>> Hi Albert!
>>
>>
>> As I understood your correctly you have run simulations with your 2
>> GPU cards on Gromacs-beta but could not do it with final version
>> havent it?
>
> not really. both versions could run with GPU. The 4.6 beta recognize my
> number of GPU as  4, but final version as 2. And the efficiency for beta is
> double comparing with final version.
>
>
>
>>
>> Could you tell me how you installed both GPU in your work-station?
>> Have you used SLI ? ( I've heard that gromacs is not suported the
>> simulation in multi-GPU regime so I'll be very happy if it's not true
>> :))
>
> both GPU version were compiled with the same command:
>
> cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC
> -DCMAKE_C_COMPILER=/soft/openmpi-1.4.3/bin/mpicc
> -DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6beta3 -DGMX_GPU=OFF
> -DBUILD_SHARED_LIBS=OFF -DCMAKE_PREFIX_PATH=/soft/fftw-3.3.3
>
> I don't think I used SLI
>
>
>>
>> Also could you tell me about configuration of your workstation in more
>> detailes ? ( what cpu and mb you  use ? )
>
> there are 16 GB for the memory,  I've got intel I7-960 for the workstation.
> I don't specify how many core should be used, but both cases occupy full CPU
> resources automatically.
>
>
>
>>
>> James
>
>
> --
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Re: [gmx-users] problems for GPU simulations

[Albert]

On 02/07/2013 11:28 AM, James Starlight wrote:

Also could you tell me what your system has performance (in gflops)
and what system you have simulated on it (average atom number,
presence of explicit membrane etc)?


it is something around 55,000 atoms with explicit membrane. I am using 
Slipids FF which is compatible with Amber FF. This is good for ligand 
topology.

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RE: [gmx-users] problems for GPU simulations

[Berk Hess]

Hi,

You don't need SLI for multi-GPU simulations in Gromacs.
But you do need a real MPI library and configure Gromacs with -DGMX_MPI=on
Then you need to start Gromacs with (depending on you MPI library):
mpirun -np #GPUs mdrun

If anything, the performance of Gromacs should have gotten better from 4.6-beta 
to 4.6, not worse.

Cheers,

Berk


> Date: Thu, 7 Feb 2013 13:28:55 +0300
> Subject: Re: [gmx-users] problems for GPU simulations
> From: jmsstarli...@gmail.com
> To: gmx-users@gromacs.org
>
> Albert,
>
> thanks for information!
>
> So now it's only intresting to my how I should install multi-GPU's on
> my system to obtain best compatibility with gromacs.
>
> Also could you tell me what your system has performance (in gflops)
> and what system you have simulated on it (average atom number,
> presence of explicit membrane etc)?
>
>
> Thank you for help again,
>
> James
>
> 2013/2/7 Albert :
> > On 02/07/2013 11:03 AM, James Starlight wrote:
> >>
> >> Hi Albert!
> >>
> >>
> >> As I understood your correctly you have run simulations with your 2
> >> GPU cards on Gromacs-beta but could not do it with final version
> >> havent it?
> >
> > not really. both versions could run with GPU. The 4.6 beta recognize my
> > number of GPU as 4, but final version as 2. And the efficiency for beta is
> > double comparing with final version.
> >
> >
> >
> >>
> >> Could you tell me how you installed both GPU in your work-station?
> >> Have you used SLI ? ( I've heard that gromacs is not suported the
> >> simulation in multi-GPU regime so I'll be very happy if it's not true
> >> :))
> >
> > both GPU version were compiled with the same command:
> >
> > cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC
> > -DCMAKE_C_COMPILER=/soft/openmpi-1.4.3/bin/mpicc
> > -DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6beta3 -DGMX_GPU=OFF
> > -DBUILD_SHARED_LIBS=OFF -DCMAKE_PREFIX_PATH=/soft/fftw-3.3.3
> >
> > I don't think I used SLI
> >
> >
> >>
> >> Also could you tell me about configuration of your workstation in more
> >> detailes ? ( what cpu and mb you use ? )
> >
> > there are 16 GB for the memory, I've got intel I7-960 for the workstation.
> > I don't specify how many core should be used, but both cases occupy full CPU
> > resources automatically.
> >
> >
> >
> >>
> >> James
> >
> >
> > --
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Re: Regarding mean square displacement

[Justin Lemkul]

On 2/6/13 11:49 PM, Kavyashree M wrote:

Dear users,

Since I am getting the mean square displacements in terms of
several nm^2. I doubt it is wrong. Could anyone please explain
me the solution for this. I checked the structure it is not denatured,
In addition I used -rmcomm in order to remove the COM movements.



Sounds like a PBC issue.  Does your dimer split across periodic boundaries?  If 
it does, then your MSD is going to go through the roof because it's measuring 
the MSD of the whole protein.


-Justin


On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M  wrote:


Dear users,

  I have a very basic question in MSD calculation.
g_msd calculation on a protein dimer (~237 aa each)
trajectory gave a plot of msd, with the values ranging
between 1 to 14nm^2.
But is this a sensible MSD? As the values given in a
paper i was referring was in Ang^2
J. Chem. Theory Comput. 2012, 8, 1129-1142

Command that i used -

echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000
-e 5 -rmcomm

Is the range of diffusion coefficient of proteins of in water l
in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)

Thank you
kavya





--


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: Error- Simulation box resizes during mdrun

[Justin Lemkul]

On 2/7/13 4:19 AM, Bharath K. Srikanth wrote:

Hi Justin:

Thanks for your reply. Yes, I did everything you mentioned. Let me explain
my steps in a bit more detail.

1) I had a lipid bilayer and a peptide from a previous simulation (in a
box 15 nm x 7.5 nm x 7.5 nm- 15 nm being perpendicular to the plane of the
bilayer). I removed the water and the peptides, so I had only the bilayer
left.

2) I then resized the box using editconf (the -box option) to a cubical
box of 7.5 nm in all directions. The bilayer remained in the center of the
new box.



But apparently you rotated the membrane, because (from the images linked below) 
the plane is now in the x-z plane, which is very atypical and prevents you from 
using semiisotropic coupling, which is normal for membrane simulations.



3) I then re-inserted the peptide by editing the coordinate file, and ran
an energy minimization. Then I added water using genbox, and ran another
EM.

4) Then I ran the simulation for 3,000,000 steps (90 ns). While this was
happening, I observed that the size of the box was beginning to change, in
the z direction (not in the y direction as I said yesterday, but still,
parallel to the plane of the bilayer).

I've included some pictures here (in the .tga format), from before and
after the simulation. When I ran it in vmd using the initial coordinates
and the trajectory file, I could actually see the box resizing during the
run.

https://www.dropbox.com/l/UJuFbDTPaISIpkSf

I'm sure there's a very simple explanation, but I can't seem to figure it
out.



It's hard to tell from the way things are rendered, but it seems to me that your 
water is very diffuse, and over the course of the simulation, the density of the 
system is increasing to try to fill a lot of void space.  A simple analysis of 
density should show this rather clearly.


-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] Re: Salt-bridge segmentation fault

[Kavyashree M]

Dear users,

After simulation dimers appear separated, I was
able to do saltbridge calculation on this. This will
be different than doing it on a dimer which are together.
Am I correct?

Please reply..
Thank you
Kavya


On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M  wrote:

> Dear users,
>
> While calculating salt bridges using g_saltbr I got
> segmentation fault when I used trajectory with only
> the protein. But when I used the trajectory with
> water It worked. But the problem was that the
> monomers were far apart in the trajectory with water
> and not with the only-protein trajectory.
>
> Kindly help!
>
> Thank you
> Kavya
>
>
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Re: [gmx-users] Re: Regarding mean square displacement

[Kavyashree M]

Dear Sir,

Thank you for the reply,

It does not cross the boundary. I made the trajectory
so that the dimers are together.

I again calculated on a superposed trajectory, Then I
got MSDs in the range of 0.01 to 0.15nm^2. But this
is still higher than the value mentioned in the paper or
is this acceptable?

Thank you
Kavya

On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul  wrote:

>
>
> On 2/6/13 11:49 PM, Kavyashree M wrote:
>
>> Dear users,
>>
>> Since I am getting the mean square displacements in terms of
>> several nm^2. I doubt it is wrong. Could anyone please explain
>> me the solution for this. I checked the structure it is not denatured,
>> In addition I used -rmcomm in order to remove the COM movements.
>>
>>
> Sounds like a PBC issue.  Does your dimer split across periodic
> boundaries?  If it does, then your MSD is going to go through the roof
> because it's measuring the MSD of the whole protein.
>
> -Justin
>
>  On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M  wrote:
>>
>>  Dear users,
>>>
>>>   I have a very basic question in MSD calculation.
>>> g_msd calculation on a protein dimer (~237 aa each)
>>> trajectory gave a plot of msd, with the values ranging
>>> between 1 to 14nm^2.
>>> But is this a sensible MSD? As the values given in a
>>> paper i was referring was in Ang^2
>>> J. Chem. Theory Comput. 2012, 8, 1129-1142
>>>
>>>
>>> Command that i used -
>>>
>>> echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000
>>> -e 5 -rmcomm
>>>
>>> Is the range of diffusion coefficient of proteins of in water l
>>> in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)
>>>
>>> Thank you
>>> kavya
>>>
>>>
>>>
>>>
> --
> ==**==
>
> 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] system far from the equilibration state

[Justin Lemkul]

On 2/7/13 4:50 AM, Shima Arasteh wrote:


Thanks for your reply.
How would I know that when I get close to the equilibration state?  By 
Pressure, Temperature,or  RMSD plots?



There are no absolutes, and it also depends on what one means by "converged" or 
"equilibrated."  If we're talking about initial NVT/NPT equilibration steps 
where the solute of interest is restrained in some way, simple analysis of 
temperature and pressure is likely sufficient to demonstrate that the ensemble 
is stable.  If we're talking about trying to determine equilibrium sampling, 
that's something else entirely and likely will involve protein-specific and/or 
lipid-specific metrics.


-Justin



Thanks in advance for your suggestions.

Sincerely,
Shima



From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Sent: Monday, February 4, 2013 11:37 PM
Subject: Re: [gmx-users] system far from the equilibration state



On 2/4/13 2:04 PM, Shima Arasteh wrote:

Hi,

I am simulating a system of peptide/membrane/water. If my system is far from 
the equilibration, would that be correct if I use Berendsen pressure coupling 
for nano seconds to do NPT equilibration and then change it to 
Parrinello-Rahman to get the true pressure? Anybody may suggest me please?



Sounds reasonable.  Berendsen is a useful method in such cases.

-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: Regarding mean square displacement

[Justin Lemkul]

On 2/7/13 6:49 AM, Kavyashree M wrote:

Dear Sir,

Thank you for the reply,

It does not cross the boundary. I made the trajectory
so that the dimers are together.

I again calculated on a superposed trajectory, Then I
got MSDs in the range of 0.01 to 0.15nm^2. But this
is still higher than the value mentioned in the paper or
is this acceptable?



Are you studying the same protein?  Given sparse detail in an email thread, not 
knowing whether the simulations were done correctly or for sufficient time, no 
one can assess correctness here.


-Justin


On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul  wrote:




On 2/6/13 11:49 PM, Kavyashree M wrote:


Dear users,

Since I am getting the mean square displacements in terms of
several nm^2. I doubt it is wrong. Could anyone please explain
me the solution for this. I checked the structure it is not denatured,
In addition I used -rmcomm in order to remove the COM movements.



Sounds like a PBC issue.  Does your dimer split across periodic
boundaries?  If it does, then your MSD is going to go through the roof
because it's measuring the MSD of the whole protein.

-Justin

  On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M  wrote:


  Dear users,


   I have a very basic question in MSD calculation.
g_msd calculation on a protein dimer (~237 aa each)
trajectory gave a plot of msd, with the values ranging
between 1 to 14nm^2.
But is this a sensible MSD? As the values given in a
paper i was referring was in Ang^2
J. Chem. Theory Comput. 2012, 8, 1129-1142


Command that i used -

echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000
-e 5 -rmcomm

Is the range of diffusion coefficient of proteins of in water l
in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)

Thank you
kavya





--
==**==

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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--


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: Salt-bridge segmentation fault

[Justin Lemkul]

On 2/7/13 6:42 AM, Kavyashree M wrote:

Dear users,

After simulation dimers appear separated, I was
able to do saltbridge calculation on this. This will
be different than doing it on a dimer which are together.
Am I correct?



Most Gromacs tools handle PBC well for simple metrics like measurements.  I 
would suspect that the seg fault comes from a mismatch in the .tpr and .xtc 
contents.  g_saltbr is a rather stupid tool that tries to guess salt bridges 
based on anything that's charged, which includes ions and other groups that 
don't necessarily participate in such interactions (see the discussion on this 
same topic in recent days).  Perhaps if g_saltbr is identifying elements that it 
wants to examine from the .tpr file but can't find them in the trajectory, you 
get a seg fault.  This shouldn't happen, but you can also use tpbconv to produce 
a subset .tpr file with just the protein for the purposes of analysis.


-Justin


On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M  wrote:


Dear users,

While calculating salt bridges using g_saltbr I got
segmentation fault when I used trajectory with only
the protein. But when I used the trajectory with
water It worked. But the problem was that the
monomers were far apart in the trajectory with water
and not with the only-protein trajectory.

Kindly help!

Thank you
Kavya




--


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: protein-ligand interactions in charmm force field

[Justin Lemkul]

On 2/7/13 5:15 AM, James Starlight wrote:

Justin,

Thanks again for suggestion. I've found that g_mindist is exactly what
I need. I'm not quite sure how I could use that tools to find all
possible interactions between my ligand and several polar residues
defined in the ndx file ( I have no problem only when I examined
manually each possible interaction separately). Finally I'm not quite


There's no way to do automated screening for these types of things.  You'll have 
to choose groups of interest and make corresponding index groups for analysis.



sure about number of contacts calculated by g_mindist. E.g I've
examined it for my ligand ( having 3 polar atoms and large hydrophobic
ring)  and 1 serine residue ( 1 polar side chain group ). As the
ouitput I've obtain 60 maximum contact number (and 10- minimum). Why
maximum number was so big ?



Sounds about right if you're using the whole serine residue, or even just its 
side chain.  The number of contacts (if memory serves, but do check the code!) 
is at most N^2, where N is the total number of atoms in both of the chosen groups.



Some another question- I want to find a way to esstimate average
mobility of my ligands in the ligand binding pocket.
For example I have 2 different complexes of my protein with 2
different ligands- one of that liugand is big and occupy big spacy
whithin protein interiour ( so that ligand is less mobile). On the
contrary the second ligand is samller and flexible so it muast be more
mobile within protein and it seen visually during visualisation of the
md trajectory. But how it could be estimated in some values ?



You can define mobility in a lot of ways - RMSF, diffusion constant, RMSD, etc.

-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] Unknown bond_atomtype CG2O2

[Justin Lemkul]

On 2/7/13 5:16 AM, Steven Neumann wrote:

Dear Gmx users,

I know this subject has been discussed but I still did not find the answer.

I have topology of my molecule:

ligand.rtp

[ GUY ] ; CGenFF output = RESI aR_citri 0.000 ! param penalty= 46.200
; charge penalty= 28.481
  [ atoms ]
C1 CG301  0.125  0
C2 CG321  -0.197 1
C3 CG321  -0.197 2
C4 CG2O2  0.848  3
O5 OG311  -0.642 4
C6 CG2O2  0.768  5
C7 CG2O2  0.768  6
O8 OG311  -0.642 7
O9 OG2D1  -0.538 8
O10OG311  -0.632 9
O11OG2D1  -0.549 10
O12OG311  -0.632 11
O13OG2D1  -0.549 12
H14HGA2   0.090  13
H15HGA2   0.090  14
H16HGA2   0.090  15
H17HGA2   0.090  16
H18HGP1   0.419  17
H19HGP1   0.430  18
H20HGP1   0.430  19
H21HGP1   0.430  20
[ bonds ]
H19O8
O8 C4
C4 O9
C4 C1
H17C3
H14C2
H20O10
O11C6
O10C6
C6 C2
C3 C7
C3 C1
C3 H16
O12H21
O12C7
C2 C1
C2 H15
C7 O13
C1 O5
O5 H18
[ impropers ]
C4 C1 O9 O8
C6 C2 O11O10
C7 C3 O13O12

Which is already in my working directory ff.

I added to ffbonded.itp

[ bondtypes ]
; i j   funcb0  kb
CG2O2  CG301  1  0.1522 167360
CG2O2  CG321  1  0.1522 167360
CG2O2  OG2D1  1  0.122  627600
CG2O2  OG311  1  0.14   192464
CG301  CG321  1  0.1538 186188
CG301  OG311  1  0.142  358150.4
CG321  HGA2   1  0. 258571.2
OG311  HGP1   1  0.096  456056
[ angletypes ]
; i j   k   functh0 cth ub0 cub
CG301  CG2O2  OG2D1  5  125.00 585.76
0.2442 16736
CG301  CG2O2  OG311  5  110.50 460.24 0
   0
CG321  CG2O2  OG2D1  5  125.00 585.76
0.2442 16736
CG321  CG2O2  OG311  5  110.50 460.24 0
   0
OG2D1  CG2O2  OG311  5  123.00 418.4
0.2262 175728
CG2O2  CG301  CG321  5  108.00 435.1360
   0
CG2O2  CG301  OG311  5  122.50 937.2160
   0
CG321  CG301  CG321  5  113.50 488.2728
0.2561 9338.688
CG321  CG301  OG311  5  110.10 633.4576   0
   0
CG2O2  CG321  CG301  5  108.00 435.1360
   0
CG2O2  CG321  HGA2   5  109.50 276.144
0.2163 25104
CG301  CG321  HGA2   5  110.10 221.752
0.2179 18853.104
HGA2   CG321  HGA2   5  109.00 297.064
0.1802 4518.72
CG2O2  OG311  HGP1   5  115.00 460.24 0
   0
CG301  OG311  HGP1   5  106.00 418.4  0
   0
[ dihedraltypes ]
; i j   k   l   funcphi0cp  mult
OG2D1  CG2O2  CG301  CG321  9  180.00
0.2092 6
OG2D1  CG2O2  CG301  OG311  9  0.00   0
   2
OG311  CG2O2  CG301  CG321  9  180.00
0.2092 6
OG311  CG2O2  CG301  OG311  9  180.00 0
   6
OG2D1  CG2O2  CG321  CG301  9  180.00 0
   6
OG2D1  CG2O2  CG321  HGA2   9  180.00 0
   6
OG311  CG2O2  CG321  CG301  9  180.00 0
   6
OG311  CG2O2  CG321  HGA2   9  180.00 0
   6
CG301  CG2O2  OG311  HGP1   9  180.00
8.5772 2
CG321  CG2O2  OG311  HGP1   9  180.00
8.5772 2
OG2D1  CG2O2  OG311  HGP1   9  180.00
8.5772 2
CG2O2  CG301  CG321  CG2O2  9  0.00
0.8368 3
CG2O2  CG301  CG321  HGA2   9  0.00
0.8368 3
CG321  CG301  CG321  CG2O2  9  180.00
0.878641
CG321  CG301  CG321  CG2O2  9  0.00
1.631762
CG321  CG301  CG321  CG2O2  9  180.00
1.4644 3
CG321  CG301  CG321  CG2O2  9  0.00
0.460244
CG321  CG301  CG321  CG2O2  9  180.00
0.376566
CG321  CG301  CG321  HGA2   9  0.00
0.815883
OG311  CG301  CG321  CG2O2  9  0.00
0.8368 3
OG311  CG301  CG321  HGA2   9  0.00
0.669443
CG2O2  CG301  OG311  HGP1   9  0.00
0.920481
CG2O2  CG301  OG31

Re: [gmx-users] MARTINI force-field in pulling simulations

[Justin Lemkul]

On 2/7/13 5:20 AM, Davide Mercadante wrote:

Dear All,

I am trying to run a pulling simulation on a small protein (18 aa) using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions NA+ and CL-.

After the equilibration I start a constant velocity pulling along the
z-direction of the last atom of the chain while the first atom is
positionally restrained in xyz (basically I am stretching the protein).
At some point from the start of the pulling simulation and before
reaching the full extension of the chain (force profile is still
steadily increasing without peaking) the simulation crashes giving me
these LINCS warnings:

Step 293252, time 5865.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.157274, max 0.291135 (between atoms 10 and 11)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length

Step 293252, time 5865.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.128562, max 0.230219 (between atoms 7 and 8)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.413291, max 0.828515 (between atoms 7 and 8)

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.587032, max 0.986890 (between atoms 11 and 13)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   7  8   46.60.2686   0.0579  0.3500
  10 11  121.30.2481   0.0550  0.3500
  13 15  168.50.2851   0.0278  0.3500

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.108373, max 0.322423 (between atoms 19 and 21)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   7  8   45.00.2686   0.0600  0.3500
  10 11   88.10.2481   0.0497  0.3500
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.330732, max 0.654588 (between atoms 23 and 25)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
  21 23   42.00.2905   0.1426  0.3500
  17 18   92.90.3146   0.1560  0.3000
  15 17   35.30.5839   0.4003  0.3500
  13 15  141.60.0278   0.2742  0.3500

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.312540, max 0.87 (between atoms 19 and 21)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   8  9   48.00.3406   0.1435  0.3100
   7  8   82.30.0579   0.4596  0.3500
  10 11  102.90.0550   0.5130  0.3500
  11 12   51.90.5425   0.3643  0.4000
  11 13   38.50.6954   0.1898  0.3500
  13 15  143.40.0278   0.2879  0.3500
  15 17   37.30.5839   0.3730  0.3500

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.343084, max 0.751867 (between atoms 3 and 5)
  17 18   93.20.3146   0.1563  0.3000
  21 23   41.60.2905   0.1443  0.3500
  23 24   33.00.3784   0.4007  0.4000
  11 13   58.20.6954   0.3283  0.3500
  23 24   33.10.3784   0.3999  0.4000
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   7  8   82.20.0579   0.4605  0.3500
   8  9   48.40.3406   0.1439  0.3100
  10 11  104.00.0550   0.5496  0.3500
  11 12   57.60.5425   0.3679  0.4000
  11 13   61.90.6954   0.1402  0.3500
  13 15  141.20.0278   0.4588  0.3500
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Step 293255, time 5865.1 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 32.745333, max 105.228383 (between atoms 17 and 18)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   5  6   30.30.3950   0.3971  0.4000
  13 15  172.90.2879   4.6287  0.3500
  15 16   33.00.2435   5.0674  0.3300
  15 17   51.20.3730  11.1793  0.3500
  17 18  107.10.1563  31.8685  0.3000
  17 19  143.40.3380  10.1576  0.3500
  

Re: [gmx-users] Re: Regarding mean square displacement

[Kavyashree M]

Dear Sir,

Yes it is the same protein. Initially I had not superposed the
structures in the trajectory. But this time I calculated the msd
on a superposed trajectory (of the same simulation). the simulation
is carried out on a dimer for 50ns using OPLS-AA and TIP4P water
model. Using Gromacs4.5.3.
If any other information is required Please let me know.

Thank you
Kavya

On Thu, Feb 7, 2013 at 5:28 PM, Justin Lemkul  wrote:

>
>
> On 2/7/13 6:49 AM, Kavyashree M wrote:
>
>> Dear Sir,
>>
>> Thank you for the reply,
>>
>> It does not cross the boundary. I made the trajectory
>> so that the dimers are together.
>>
>> I again calculated on a superposed trajectory, Then I
>> got MSDs in the range of 0.01 to 0.15nm^2. But this
>> is still higher than the value mentioned in the paper or
>> is this acceptable?
>>
>>
> Are you studying the same protein?  Given sparse detail in an email
> thread, not knowing whether the simulations were done correctly or for
> sufficient time, no one can assess correctness here.
>
> -Justin
>
>  On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/6/13 11:49 PM, Kavyashree M wrote:
>>>
>>>  Dear users,

 Since I am getting the mean square displacements in terms of
 several nm^2. I doubt it is wrong. Could anyone please explain
 me the solution for this. I checked the structure it is not denatured,
 In addition I used -rmcomm in order to remove the COM movements.


  Sounds like a PBC issue.  Does your dimer split across periodic
>>> boundaries?  If it does, then your MSD is going to go through the roof
>>> because it's measuring the MSD of the whole protein.
>>>
>>> -Justin
>>>
>>>   On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M 
>>> wrote:
>>>

   Dear users,

>
>I have a very basic question in MSD calculation.
> g_msd calculation on a protein dimer (~237 aa each)
> trajectory gave a plot of msd, with the values ranging
> between 1 to 14nm^2.
> But is this a sensible MSD? As the values given in a
> paper i was referring was in Ang^2
> J. Chem. Theory Comput. 2012, 8, 1129-1142
>
>
> Command that i used -
>
> echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b
> 4000
> -e 5 -rmcomm
>
> Is the range of diffusion coefficient of proteins of in water l
> in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)
>
> Thank you
> kavya
>
>
>
>
>  --
>>> ====
>>>
>>>
>>> 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>
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>>> Support/Mailing_Lists/Search>> Mailing_Lists/Search>before
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>>>
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>>> 
>>> >
>>>
>>>
> --
> ==**==
>
> 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: Salt-bridge segmentation fault

[Kavyashree M]

Thank you,

I have noticed this in the output of the g_saltbr. Later
I separated the files according to what ever I require.
My worry was only that of the dimeric interface which
could not be seen because it is separated.

I will try by giving a separate tpr file without water.

Thank you
Kavya


On Thu, Feb 7, 2013 at 5:31 PM, Justin Lemkul  wrote:

>
>
> On 2/7/13 6:42 AM, Kavyashree M wrote:
>
>> Dear users,
>>
>> After simulation dimers appear separated, I was
>> able to do saltbridge calculation on this. This will
>> be different than doing it on a dimer which are together.
>> Am I correct?
>>
>>
> Most Gromacs tools handle PBC well for simple metrics like measurements.
>  I would suspect that the seg fault comes from a mismatch in the .tpr and
> .xtc contents.  g_saltbr is a rather stupid tool that tries to guess salt
> bridges based on anything that's charged, which includes ions and other
> groups that don't necessarily participate in such interactions (see the
> discussion on this same topic in recent days).  Perhaps if g_saltbr is
> identifying elements that it wants to examine from the .tpr file but can't
> find them in the trajectory, you get a seg fault.  This shouldn't happen,
> but you can also use tpbconv to produce a subset .tpr file with just the
> protein for the purposes of analysis.
>
> -Justin
>
>
>  On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M  wrote:
>>
>>  Dear users,
>>>
>>> While calculating salt bridges using g_saltbr I got
>>> segmentation fault when I used trajectory with only
>>> the protein. But when I used the trajectory with
>>> water It worked. But the problem was that the
>>> monomers were far apart in the trajectory with water
>>> and not with the only-protein trajectory.
>>>
>>> Kindly help!
>>>
>>> Thank you
>>> Kavya
>>>
>>>
>>>
> --
> ==**==
>
> 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] problems for GPU simulations

[Szilárd Páll]

On Thu, Feb 7, 2013 at 10:16 AM, Albert  wrote:

> Hello:
>
>  I got a workstation with two GTX590 which have two core for each GPU. I
> can submit gromacs GPU jobs with command:
>
> mpirun  -np 4 mdrun .
>
> with such running, I can get 26ns/day for Gromacs-4.6 beta version.
>
> However, I found that for Gromacs-4.6 final version (which is the latest
> one), it claimed that I only have two GPU, it asked me to adjust -np to 2.
>

Please make sure that nvididia-smi or the deviceQuery SDK tool show all
four GPUs. If that is the case and mdrun still shows only two, please file
a bug report with you OS info and a log file attached.

Cheers,
--
Szilárd



>
> so I submit the jobs with command:
>
> mpirun -np 2 mdrun...
>
> for the same system with the same paramters (of course the tpr file must
> be regenerated). I found that I can get only half of the speed, something
> around 10 ns/day.
>
>
> So I am just wondering what's happening?
>
> thank you very much
> best
> Albert
> --
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Re: [gmx-users] Re: Regarding mean square displacement

[Justin Lemkul]

On 2/7/13 7:08 AM, Kavyashree M wrote:

Dear Sir,

Yes it is the same protein. Initially I had not superposed the
structures in the trajectory. But this time I calculated the msd
on a superposed trajectory (of the same simulation). the simulation
is carried out on a dimer for 50ns using OPLS-AA and TIP4P water
model. Using Gromacs4.5.3.
If any other information is required Please let me know.



The specific suitability of a protocol is dependent upon what you believe to be 
correct for your system based on precedent and chemical knowledge.  Also be 
aware that post-processing of the trajectory to superimpose frames defeats the 
purpose of measuring diffusion - if you re-center or superimpose your 
structures, it's not diffusing!  Dealing with a dimeric protein may be a 
challenge for which g_msd wasn't designed, so I don't know if there's an easy 
solution here.  Perhaps someone else can suggest something.


-Justin


Thank you
Kavya

On Thu, Feb 7, 2013 at 5:28 PM, Justin Lemkul  wrote:




On 2/7/13 6:49 AM, Kavyashree M wrote:


Dear Sir,

Thank you for the reply,

It does not cross the boundary. I made the trajectory
so that the dimers are together.

I again calculated on a superposed trajectory, Then I
got MSDs in the range of 0.01 to 0.15nm^2. But this
is still higher than the value mentioned in the paper or
is this acceptable?



Are you studying the same protein?  Given sparse detail in an email
thread, not knowing whether the simulations were done correctly or for
sufficient time, no one can assess correctness here.

-Justin

  On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul  wrote:





On 2/6/13 11:49 PM, Kavyashree M wrote:

  Dear users,


Since I am getting the mean square displacements in terms of
several nm^2. I doubt it is wrong. Could anyone please explain
me the solution for this. I checked the structure it is not denatured,
In addition I used -rmcomm in order to remove the COM movements.


  Sounds like a PBC issue.  Does your dimer split across periodic

boundaries?  If it does, then your MSD is going to go through the roof
because it's measuring the MSD of the whole protein.

-Justin

   On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M 
wrote:



   Dear users,



I have a very basic question in MSD calculation.
g_msd calculation on a protein dimer (~237 aa each)
trajectory gave a plot of msd, with the values ranging
between 1 to 14nm^2.
But is this a sensible MSD? As the values given in a
paper i was referring was in Ang^2
J. Chem. Theory Comput. 2012, 8, 1129-1142


Command that i used -

echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b
4000
-e 5 -rmcomm

Is the range of diffusion coefficient of proteins of in water l
in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)

Thank you
kavya




  --

====


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>




====

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--
==**==

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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--


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

Re: [gmx-users] Re: Regarding mean square displacement

[Kavyashree M]

Thank you,

My intention is mainly to compare the MSDs of the
trajectory and not the diffusion as such. The paper I
mentioned have used a tetramer for the similar analysis.
Hence I wanted to know whether the values I obtained
is sensible.

Thank you
Kavya

On Thu, Feb 7, 2013 at 7:25 PM, Justin Lemkul  wrote:

>
>
> On 2/7/13 7:08 AM, Kavyashree M wrote:
>
>> Dear Sir,
>>
>> Yes it is the same protein. Initially I had not superposed the
>> structures in the trajectory. But this time I calculated the msd
>> on a superposed trajectory (of the same simulation). the simulation
>> is carried out on a dimer for 50ns using OPLS-AA and TIP4P water
>> model. Using Gromacs4.5.3.
>> If any other information is required Please let me know.
>>
>>
> The specific suitability of a protocol is dependent upon what you believe
> to be correct for your system based on precedent and chemical knowledge.
>  Also be aware that post-processing of the trajectory to superimpose frames
> defeats the purpose of measuring diffusion - if you re-center or
> superimpose your structures, it's not diffusing!  Dealing with a dimeric
> protein may be a challenge for which g_msd wasn't designed, so I don't know
> if there's an easy solution here.  Perhaps someone else can suggest
> something.
>
> -Justin
>
>  Thank you
>> Kavya
>>
>> On Thu, Feb 7, 2013 at 5:28 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/7/13 6:49 AM, Kavyashree M wrote:
>>>
>>>  Dear Sir,

 Thank you for the reply,

 It does not cross the boundary. I made the trajectory
 so that the dimers are together.

 I again calculated on a superposed trajectory, Then I
 got MSDs in the range of 0.01 to 0.15nm^2. But this
 is still higher than the value mentioned in the paper or
 is this acceptable?


  Are you studying the same protein?  Given sparse detail in an email
>>> thread, not knowing whether the simulations were done correctly or for
>>> sufficient time, no one can assess correctness here.
>>>
>>> -Justin
>>>
>>>   On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul  wrote:
>>>



> On 2/6/13 11:49 PM, Kavyashree M wrote:
>
>   Dear users,
>
>>
>> Since I am getting the mean square displacements in terms of
>> several nm^2. I doubt it is wrong. Could anyone please explain
>> me the solution for this. I checked the structure it is not denatured,
>> In addition I used -rmcomm in order to remove the COM movements.
>>
>>
>>   Sounds like a PBC issue.  Does your dimer split across periodic
>>
> boundaries?  If it does, then your MSD is going to go through the roof
> because it's measuring the MSD of the whole protein.
>
> -Justin
>
>On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M 
> wrote:
>
>
>>Dear users,
>>
>>
>>> I have a very basic question in MSD calculation.
>>> g_msd calculation on a protein dimer (~237 aa each)
>>> trajectory gave a plot of msd, with the values ranging
>>> between 1 to 14nm^2.
>>> But is this a sensible MSD? As the values given in a
>>> paper i was referring was in Ang^2
>>> J. Chem. Theory Comput. 2012, 8, 1129-1142
>>>
>>>
>>> Command that i used -
>>>
>>> echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b
>>> 4000
>>> -e 5 -rmcomm
>>>
>>> Is the range of diffusion coefficient of proteins of in water l
>>> in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)
>>>
>>> Thank you
>>> kavya
>>>
>>>
>>>
>>>
>>>   --
>>>
>> ==**==
>
>
>
> 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://vt.edu/Pages/Personal/**justin
> >
>  http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justin
> >
>
>>
>>
> ==**==
>
>
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Re: [gmx-users] united atom

[Justin Lemkul]

On 2/7/13 9:46 AM, Ali Alizadeh wrote:

Dear All user

There are 350 decane molecules in my simulation box,

I like doing a simulation(npt ensemble) by a united atom force field,
Can I use the opls (nonbonded: L-J 6-12 and coloumb) that is in
gromacs?

Beside, How can I neglect  coloumb interaction(non-bonded) and
dihedrals(bonded)?



The OPLS force field in Gromacs contains both OPLS-AA (all-atom) and OPLS-UA 
(united-atom) types, so you could in theory use OPLS-UA, but that's a fairly 
ancient force field.  In that case, there are no Coulombic interactions anyway, 
because the united-atom carbons should not have any charge.  If you want to 
neglect dihedrals, I think you're hacking the force field in a way that makes no 
sense.


-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] The time for the temperature and pressure coupling

[Michael Shirts]

Ah, now perhaps I see that I misread the question - it could have been
phrased more clearly.  If Erik understood it correctly, then the
answer to the question is: It depends on the integrator.  The
simulation is not constrained to a particular temperature or pressure
- rather, the dynamics are modified such that the ensemble is
consistent with the external temperature and pressure are specified.
Exactly where in the integration routine the dynamics are modified
depends on the method used.  See the manual for more of the details!

On Thu, Feb 7, 2013 at 3:59 AM, Erik Marklund  wrote:
> Hi,
>
> Perhaps a side point: Temperature and pressure can not be seen as
> constraints to the system at any given instant in the sense that e.g. the
> instantaneous kinetic energy perfectly match the temperature at every time
> step just because you have a thermostat. Time and ensemble averages will,
> however, reflect the temperature and pressure coupling.
>
> Erik
>
>
> On Feb 6, 2013, at 11:28 PM, Bao Kai wrote:
>
>> Dear Gromacs Team,
>>
>> I have a small question related to the scheme of the MD in Gromacs.
>>
>> When are the temperature and pressure constrains are enforced, before
>> the update of the velocity and position or after?
>>
>> Thank you very much.
>>
>> Best Regards,
>> Kai
>> --
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Re: [gmx-users] Re:united atom

[Justin Lemkul]

On 2/7/13 10:43 AM, Ali Alizadeh wrote:

Dear Justin

Thank you for your reply,

I want to use Nose-Hoover thermostat and MTTK barostat and shake
algorithm and md-vv integrator,

but I got this error:

---
Fatal error:
SHAKE is not supported with domain decomposition and constraint that
cross charge group boundaries, use LINCS
--



Then clearly your combination of parameters is unsupported.  Do as the error 
message says, or perhaps trying running using particle decomposition (mdrun 
-pd), which will be slower than DD.


-Justin


A part of my topology file:
--
[ moleculetype ]
; Namenrexcl
DECANE  9

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
; residue   0 LI  rtp LI   q  0.0
  1   opls_071  0 LI C1  1  0 14.027   ; qtot 0
  2   opls_071  0 LI C2  2  0 14.027   ; qtot 0
  3   opls_071  0 LI C3  3  0 14.027   ; qtot 0
  4   opls_071  0 LI C4  4  0 14.027   ; qtot 0
  5   opls_071  0 LI C5  5  0 14.027   ; qtot 0
  6   opls_071  0 LI C6  6  0 14.027   ; qtot 0
  7   opls_068  0 LI C7  7  0 15.035   ; qtot 0
  8   opls_071  0 LI C8  8  0 14.027   ; qtot 0
  9   opls_068  0 LI C9  9  0 15.035   ; qtot 0
 10   opls_071  0 LIC10  10  0 14.027   ; qtot 0

---


On 2/7/13 9:46 AM, Ali Alizadeh wrote:

Dear All user

There are 350 decane molecules in my simulation box,

I like doing a simulation(npt ensemble) by a united atom force field,
Can I use the opls (nonbonded: L-J 6-12 and coloumb) that is in
gromacs?

Beside, How can I neglect  coloumb interaction(non-bonded) and
dihedrals(bonded)?




The OPLS force field in Gromacs contains both OPLS-AA (all-atom) and OPLS-UA
(united-atom) types, so you could in theory use OPLS-UA, but that's a fairly
ancient force field.  In that case, there are no Coulombic interactions anyway,
because the united-atom carbons should not have any charge.  If you want to
neglect dihedrals, I think you're hacking the force field in a way that makes no
sense.



-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] problems for GPU simulations

[Albert]

On 02/07/2013 01:34 PM, Szilárd Páll wrote:

Please make sure that nvididia-smi or the deviceQuery SDK tool show all
four GPUs. If that is the case and mdrun still shows only two, please file
a bug report with you OS info and a log file attached.

Cheers,
--
Szilárd


no, it showed two. I don't know why it only work in beta version it can 
recognize 4 GPU, but in final version only 2 The fact is that the 
beta version use -np 4 can get double speed. The GTX590 have two core, 
so two GPU have 4 core.



here is the log for nvidia-sim:

Thu Feb  7 17:27:10 2013
+--+
| NVIDIA-SMI 2.285.05   Driver Version: 285.05.33 |
|---+--+--+
| Nb.  Name | Bus IdDisp.  | Volatile ECC SB 
/ DB |
| Fan   Temp   Power Usage /Cap | Memory Usage | GPU Util. 
Compute M. |

|===+==+==|
| 0.  GeForce GTX 590   | :0C:00.0  N/A| N/AN/A |
|   0%   55 C  N/A   N/A /  N/A |  22%  336MB / 1535MB |  N/A Default|
|---+--+--|
| 1.  GeForce GTX 590   | :0B:00.0  N/A| N/AN/A |
|  43%   57 C  N/A   N/A /  N/A |   0%5MB / 1535MB |  N/A Default|
|---+--+--|
| Compute processes: GPU Memory |
|  GPU  PID Process name Usage  |
|=|
|  0.   ERROR: Not 
Supported  |
|  1.   ERROR: Not 
Supported  |

+-+




here is the log for mdrun:


Program mdrun_mpi, VERSION 4.6
Source code file: 
/home/albert/Documents/2013-02-06/gromacs-4.6/src/gmxlib/gmx_detect_hardware.c, 
line: 356


Fatal error:
Incorrect launch configuration: mismatching number of PP MPI processes 
and GPUs per node.
mdrun_mpi was started with 4 PP MPI processes per node, but only 2 GPUs 
were detected.

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

"I Like You. I Will Kill You Last" (Tyler in Fishtank)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 4

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[gmx-users] Re:united atom

[ABEL Stephane 175950]

Hello, 

Is it correct for you that in your topolgy file, some atoms have wrong  mass 
(i.e. C7 and C9 have a mass of 15.035 instead of 14.027) in your DECAN  
molecule ? Are they at the end ? 

Stephane 


--

Message: 3
Date: Thu, 7 Feb 2013 19:13:11 +0330
From: Ali Alizadeh 
Subject: [gmx-users] Re:united atom
To: gmx-users 
Message-ID:

Content-Type: text/plain; charset=UTF-8

Dear Justin

Thank you for your reply,

I want to use Nose-Hoover thermostat and MTTK barostat and shake
algorithm and md-vv integrator,

but I got this error:

---
Fatal error:
SHAKE is not supported with domain decomposition and constraint that
cross charge group boundaries, use LINCS
--

A part of my topology file:
--
[ moleculetype ]
; Namenrexcl
DECANE  9

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
; residue   0 LI  rtp LI   q  0.0
 1   opls_071  0 LI C1  1  0 14.027   ; qtot 0
 2   opls_071  0 LI C2  2  0 14.027   ; qtot 0
 3   opls_071  0 LI C3  3  0 14.027   ; qtot 0
 4   opls_071  0 LI C4  4  0 14.027   ; qtot 0
 5   opls_071  0 LI C5  5  0 14.027   ; qtot 0
 6   opls_071  0 LI C6  6  0 14.027   ; qtot 0
 7   opls_068  0 LI C7  7  0 15.035   ; qtot 0
 8   opls_071  0 LI C8  8  0 14.027   ; qtot 0
 9   opls_068  0 LI C9  9  0 15.035   ; qtot 0
10   opls_071  0 LIC10  10  0 14.027   ; qtot 0

---


On 2/7/13 9:46 AM, Ali Alizadeh wrote:
> Dear All user
>
> There are 350 decane molecules in my simulation box,
>
> I like doing a simulation(npt ensemble) by a united atom force field,
> Can I use the opls (nonbonded: L-J 6-12 and coloumb) that is in
> gromacs?
>
> Beside, How can I neglect  coloumb interaction(non-bonded) and
> dihedrals(bonded)?
>

>>The OPLS force field in Gromacs contains both OPLS-AA (all-atom) and OPLS-UA
>>(united-atom) types, so you could in theory use OPLS-UA, but that's a fairly
>>ancient force field.  In that case, there are no Coulombic interactions 
>>anyway,
>>because the united-atom carbons should not have any charge.  If you want to
>>neglect dihedrals, I think you're hacking the force field in a way that makes 
>>no
>>sense.

>>-Justin

--
Sincerely

Ali Alizadeh
University of Tehran
College of engineering(Fanni)
Department of chemical engineering
IPE (Institute of Petroleum Engineering)
M.Sc Candidate, class of 2013
B.Sc Graduate 2011(University of Tehran,Fanni)

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Re: [gmx-users] g_wham missing option

[Jochen Hub]

Hi Anthony,

just one remark here: Make sure you have always a couple of histograms 
overlapping each other (maybe 5-10). If every histogram overlaps only 
with two neighbors, you will severely underestimate the error.


Hence, to estimate the error, you need rather many histograms from many 
short umbrella simulations than few histograms from few long umbrella 
simulations.


Cheers,
Jochen


Am 2/3/13 11:43 AM, schrieb Nash, Anthony:

Hi Justin,

Thanks for the reply. You were spot on about the version difference.

Thanks again.
Anthony

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: 02 February 2013 18:06
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_wham missing option

On 2/2/13 12:58 PM, Nash, Anthony wrote:

Hi All,

I am using Gromacs 4.5.5 and running free energy calculations. According to the article 
"g_wham - A Free Weighted Histogram.." (J. Chem. Theory. Comput. 2010, 6, 
3713-3720), there is the option -bs-method. However, I am unable to find this option when 
running g_wham. I want to use bayesian bootstraps of complete histograms.

I have a feeling I am missing something completely obvious. Any help would be 
appreciated.



Take a closer look at g_wham -h.  The option you're asking about is definitely
there.  Also be sure you're using the version you think you are; g_wham was
overhauled between 4.0.7 and 4.5.

-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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--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
---
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Re: [gmx-users] configure gromacs 4.6

[jeela keel]

Hi All,

Thank you for the help. But I am not sure how to use cmake??  Do I need to
make  a new directory something like the following, or just in the gromacs
directory?

mkdir cmake
cd cmake

cmake -DCMAKE_PREFIX_PATH=/home/jeela/local/gromacs-4.6
--program-suffix=-4.6 --with-fft=fftw3

Thank you and kind regards.

Jeela


On Wed, Feb 6, 2013 at 4:01 PM, Roland Schulz  wrote:

> On Wed, Feb 6, 2013 at 6:05 PM, jeela keel  wrote:
>
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON
> >
>
> Because you already build fftw yourself you don't need GMX_BUILD_OWN_FFTW.
> The option means that gromacs builds fftw for you. Instead simply specify
> where you installed fftw with CMAKE_PREFIX_PATH
>
> Roland
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] Protein unfolded after COM pulling

[Yun Shi]

A general question:

In COM pulling (pull two molecules away), does the weakest
inter-molecular interaction always break first? Or is it the
interaction aligned on the pulling direction break first?

In other words, does every part of the molecule "feel" the pulling
force? Or the part close to the COM "feel" stronger force that the
part of molecule that is far away from its COM?

Thanks,
Yun

On Mon, Feb 4, 2013 at 6:35 PM, Justin Lemkul  wrote:
>
>
> On 2/4/13 9:32 PM, Yun Shi wrote:
>>
>> Hi all,
>>
>> I am pulling one monomer of a tetrameric protein away from the other
>> three monomers with pull_k1 = 1 and pull_rate1 = 0.0005.
>>
>> As shown in the attached picture, the green monomer (being pulled) has
>> unfolded while two regions on it are still interacting with the other
>> three monomers at the end of my pulling simulations (13 ns, so COM
>> distance has been pulled 6.5 nm).
>>
>
> Attachments to the list are prohibited; if you have files or images to share
> you must provide a URL.
>
>
>> If I want to calculate deltaG of this process, can I use distance
>> restraints on the green monomer being pulled to maintain its folded
>> structure? Otherwise, I will have to construct a larger box or pull
>> even slower than 0.5 nm/ns.
>>
>
> Yes, you probably need distance restraints.  Complex restraints often fail
> with domain decomposition, so you may need to use particle decomposition
> instead.
>
> -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] configure gromacs 4.6

[Justin Lemkul]

On 2/7/13 12:39 PM, jeela keel wrote:

Hi All,

Thank you for the help. But I am not sure how to use cmake??  Do I need to
make  a new directory something like the following, or just in the gromacs
directory?

mkdir cmake
cd cmake

cmake -DCMAKE_PREFIX_PATH=/home/jeela/local/gromacs-4.6
--program-suffix=-4.6 --with-fft=fftw3



Most of these options are incorrect.  The autotools and CMake build processes 
are very different.  Please refer to the website for detailed instructions.


http://www.gromacs.org/Documentation/Installation_Instructions#4._Doing_a_build_of_GROMACS

-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] Protein unfolded after COM pulling

[Justin Lemkul]

On 2/7/13 12:40 PM, Yun Shi wrote:

A general question:

In COM pulling (pull two molecules away), does the weakest
inter-molecular interaction always break first? Or is it the
interaction aligned on the pulling direction break first?



Probably both.  Whatever you do with SMD is path-dependent.


In other words, does every part of the molecule "feel" the pulling
force? Or the part close to the COM "feel" stronger force that the
part of molecule that is far away from its COM?



Forces are interpolated onto other parts of the structure, but as stated above, 
whichever way you pull has implications for the outcome.  It's not an 
equilibrium process.


-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] MARTINI force-field in pulling simulations

[Davide Mercadante]

Dear Justin, 

Thank you for your reply. I decreased the time step from 0.02 to 0.005 and
run the simulation again. The simulation still crashes giving LINCS
warning on the same atoms but does it later.
Do you advice to keep reducing the time step in order to reach a simulated
time where the pull of the whole molecule occurs and I see the force
peaking? I am still not sure why this happens...

Thanks. 

Davide

On 7/02/13 1:05 PM, "Justin Lemkul"  wrote:

>
>
>On 2/7/13 5:20 AM, Davide Mercadante wrote:
>> Dear All,
>>
>> I am trying to run a pulling simulation on a small protein (18 aa) using
>> the GC forcefield MARTINI (v2.2). I have energy minimized and
>> equilibrated (NPT) my system and everything seems fine. My system
>> consists of the protein + water + ions NA+ and CL-.
>>
>> After the equilibration I start a constant velocity pulling along the
>> z-direction of the last atom of the chain while the first atom is
>> positionally restrained in xyz (basically I am stretching the protein).
>> At some point from the start of the pulling simulation and before
>> reaching the full extension of the chain (force profile is still
>> steadily increasing without peaking) the simulation crashes giving me
>> these LINCS warnings:
>>
>> Step 293252, time 5865.04 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.157274, max 0.291135 (between atoms 10 and 11)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>
>> Step 293252, time 5865.04 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.128562, max 0.230219 (between atoms 7 and 8)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>
>> Step 293253, time 5865.06 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.413291, max 0.828515 (between atoms 7 and 8)
>>
>> Step 293253, time 5865.06 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.587032, max 0.986890 (between atoms 11 and 13)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>7  8   46.60.2686   0.0579  0.3500
>>   10 11  121.30.2481   0.0550  0.3500
>>   13 15  168.50.2851   0.0278  0.3500
>>
>> Step 293253, time 5865.06 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.108373, max 0.322423 (between atoms 19 and 21)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>7  8   45.00.2686   0.0600  0.3500
>>   10 11   88.10.2481   0.0497  0.3500
>> Wrote pdb files with previous and current coordinates
>> Wrote pdb files with previous and current coordinates
>>
>> Step 293254, time 5865.08 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.330732, max 0.654588 (between atoms 23 and 25)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>   21 23   42.00.2905   0.1426  0.3500
>>   17 18   92.90.3146   0.1560  0.3000
>>   15 17   35.30.5839   0.4003  0.3500
>>   13 15  141.60.0278   0.2742  0.3500
>>
>> Step 293254, time 5865.08 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.312540, max 0.87 (between atoms 19 and 21)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>8  9   48.00.3406   0.1435  0.3100
>>7  8   82.30.0579   0.4596  0.3500
>>   10 11  102.90.0550   0.5130  0.3500
>>   11 12   51.90.5425   0.3643  0.4000
>>   11 13   38.50.6954   0.1898  0.3500
>>   13 15  143.40.0278   0.2879  0.3500
>>   15 17   37.30.5839   0.3730  0.3500
>>
>> Step 293254, time 5865.08 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.343084, max 0.751867 (between atoms 3 and 5)
>>   17 18   93.20.3146   0.1563  0.3000
>>   21 23   41.60.2905   0.1443  0.3500
>>   23 24   33.00.3784   0.4007  0.4000
>>   11 13   58.20.6954   0.3283  0.3500
>>   23 24   33.10.3784   0.3999  0.4000
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>7  8   82.20.0579   0.4605  0.3500
>>8  9   48.40.3406   0.1439  0.3100
>>   10 11  104.00.0550   0.5496  0.3500
>>   11 12   57.60.5425   0.3679  0.4000
>>   11 13   61.90.6954   0.1402  0.3500
>>   13 15  141.20.0278   0.4588  0.3500
>> Wrote pd

Re: [gmx-users] MARTINI force-field in pulling simulations

[Justin Lemkul]

On 2/7/13 1:44 PM, Davide Mercadante wrote:

Dear Justin,

Thank you for your reply. I decreased the time step from 0.02 to 0.005 and
run the simulation again. The simulation still crashes giving LINCS
warning on the same atoms but does it later.
Do you advice to keep reducing the time step in order to reach a simulated
time where the pull of the whole molecule occurs and I see the force
peaking? I am still not sure why this happens...



No, I think the issue is probably more fundamental.  MARTINI uses fixed 
secondary structure (bonds in the topology to preserve geometry).  You're 
probably just pulling against those and the algorithms that work on bonded 
interactions are failing.


-Justin


Thanks.

Davide

On 7/02/13 1:05 PM, "Justin Lemkul"  wrote:




On 2/7/13 5:20 AM, Davide Mercadante wrote:

Dear All,

I am trying to run a pulling simulation on a small protein (18 aa) using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions NA+ and CL-.

After the equilibration I start a constant velocity pulling along the
z-direction of the last atom of the chain while the first atom is
positionally restrained in xyz (basically I am stretching the protein).
At some point from the start of the pulling simulation and before
reaching the full extension of the chain (force profile is still
steadily increasing without peaking) the simulation crashes giving me
these LINCS warnings:

Step 293252, time 5865.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.157274, max 0.291135 (between atoms 10 and 11)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length

Step 293252, time 5865.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.128562, max 0.230219 (between atoms 7 and 8)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.413291, max 0.828515 (between atoms 7 and 8)

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.587032, max 0.986890 (between atoms 11 and 13)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
7  8   46.60.2686   0.0579  0.3500
   10 11  121.30.2481   0.0550  0.3500
   13 15  168.50.2851   0.0278  0.3500

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.108373, max 0.322423 (between atoms 19 and 21)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
7  8   45.00.2686   0.0600  0.3500
   10 11   88.10.2481   0.0497  0.3500
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.330732, max 0.654588 (between atoms 23 and 25)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
   21 23   42.00.2905   0.1426  0.3500
   17 18   92.90.3146   0.1560  0.3000
   15 17   35.30.5839   0.4003  0.3500
   13 15  141.60.0278   0.2742  0.3500

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.312540, max 0.87 (between atoms 19 and 21)
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
8  9   48.00.3406   0.1435  0.3100
7  8   82.30.0579   0.4596  0.3500
   10 11  102.90.0550   0.5130  0.3500
   11 12   51.90.5425   0.3643  0.4000
   11 13   38.50.6954   0.1898  0.3500
   13 15  143.40.0278   0.2879  0.3500
   15 17   37.30.5839   0.3730  0.3500

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.343084, max 0.751867 (between atoms 3 and 5)
   17 18   93.20.3146   0.1563  0.3000
   21 23   41.60.2905   0.1443  0.3500
   23 24   33.00.3784   0.4007  0.4000
   11 13   58.20.6954   0.3283  0.3500
   23 24   33.10.3784   0.3999  0.4000
bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
7  8   82.20.0579   0.4605  0.3500
8  9   48.40.3406   0.1439  0.3100
   10 11  104.00.0550   0.5496  0.3500
   11 12   57.60.5425   0.3679  0.4000
   11 13   61.90.6954   0.14

Re: [gmx-users] Many energygrps to output

[Justin Lemkul]

On 2/7/13 2:13 PM, Yun Shi wrote:

Hi all,

I want to rerun a trajectory to calculate interaction energies between
each residue of protein A and protein B. In other words, I want to
calculate interaction energies for pairs A1 - B, A2-B, A3-B, A4-B...,
A399-B.

So instead of making an index file with 399 groups of each residue in
A and typing in rerun.mdp file 400 group names as
"energygrps = A1 A2 A3 A4 ... A399 B", and issuing g_energy command 399 times,



Writing such lines could probably be scripted in a loop of your favorite 
programming language, but be aware that your .edr file is going to become 
enormous, probably several GB, depending on the length of the trajectory.  You 
won't have 400 energy terms, you will have 400*400 energy terms.



is there an easier way to do this in Gromacs?



Not in Gromacs, but using scripts to call Gromacs functions and/or write lines 
to files, yes.


-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] MARTINI force-field in pulling simulations

[Davide Mercadante]

Thank you Justin, 

I guess this means that this kind of simulations is not possible without a
modification of the forcefield (which would ultimately mean using a
different forcefield I believe)?

Thanks. 

Cheers,
Davide

On 7/02/13 8:09 PM, "Justin Lemkul"  wrote:

>
>
>On 2/7/13 1:44 PM, Davide Mercadante wrote:
>> Dear Justin,
>>
>> Thank you for your reply. I decreased the time step from 0.02 to 0.005
>>and
>> run the simulation again. The simulation still crashes giving LINCS
>> warning on the same atoms but does it later.
>> Do you advice to keep reducing the time step in order to reach a
>>simulated
>> time where the pull of the whole molecule occurs and I see the force
>> peaking? I am still not sure why this happens...
>>
>
>No, I think the issue is probably more fundamental.  MARTINI uses fixed
>secondary structure (bonds in the topology to preserve geometry).  You're
>probably just pulling against those and the algorithms that work on
>bonded 
>interactions are failing.
>
>-Justin
>
>> Thanks.
>>
>> Davide
>>
>> On 7/02/13 1:05 PM, "Justin Lemkul"  wrote:
>>
>>>
>>>
>>> On 2/7/13 5:20 AM, Davide Mercadante wrote:
 Dear All,

 I am trying to run a pulling simulation on a small protein (18 aa)
using
 the GC forcefield MARTINI (v2.2). I have energy minimized and
 equilibrated (NPT) my system and everything seems fine. My system
 consists of the protein + water + ions NA+ and CL-.

 After the equilibration I start a constant velocity pulling along the
 z-direction of the last atom of the chain while the first atom is
 positionally restrained in xyz (basically I am stretching the
protein).
 At some point from the start of the pulling simulation and before
 reaching the full extension of the chain (force profile is still
 steadily increasing without peaking) the simulation crashes giving me
 these LINCS warnings:

 Step 293252, time 5865.04 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.157274, max 0.291135 (between atoms 10 and 11)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length

 Step 293252, time 5865.04 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.128562, max 0.230219 (between atoms 7 and 8)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length

 Step 293253, time 5865.06 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.413291, max 0.828515 (between atoms 7 and 8)

 Step 293253, time 5865.06 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.587032, max 0.986890 (between atoms 11 and 13)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 7  8   46.60.2686   0.0579  0.3500
10 11  121.30.2481   0.0550  0.3500
13 15  168.50.2851   0.0278  0.3500

 Step 293253, time 5865.06 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.108373, max 0.322423 (between atoms 19 and 21)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 7  8   45.00.2686   0.0600  0.3500
10 11   88.10.2481   0.0497  0.3500
 Wrote pdb files with previous and current coordinates
 Wrote pdb files with previous and current coordinates

 Step 293254, time 5865.08 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.330732, max 0.654588 (between atoms 23 and 25)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
21 23   42.00.2905   0.1426  0.3500
17 18   92.90.3146   0.1560  0.3000
15 17   35.30.5839   0.4003  0.3500
13 15  141.60.0278   0.2742  0.3500

 Step 293254, time 5865.08 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.312540, max 0.87 (between atoms 19 and 21)
 bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 8  9   48.00.3406   0.1435  0.3100
 7  8   82.30.0579   0.4596  0.3500
10 11  102.90.0550   0.5130  0.3500
11 12   51.90.5425   0.3643  0.4000
11 13   38.50.6954   0.1898  0.3500
13 15  143.40.0278   0.2879  0.3500
15 17   37.30.5839   0.3730  0.3500

 Step 293254, time 5865.08 (ps)  LINCS WARNING
 relative constraint devi

Re: [gmx-users] MARTINI force-field in pulling simulations

[Justin Lemkul]

On 2/7/13 2:29 PM, Davide Mercadante wrote:

Thank you Justin,

I guess this means that this kind of simulations is not possible without a
modification of the forcefield (which would ultimately mean using a
different forcefield I believe)?



If you're looking to unfold secondary structure elements, yes.

-Justin


Thanks.

Cheers,
Davide

On 7/02/13 8:09 PM, "Justin Lemkul"  wrote:




On 2/7/13 1:44 PM, Davide Mercadante wrote:

Dear Justin,

Thank you for your reply. I decreased the time step from 0.02 to 0.005
and
run the simulation again. The simulation still crashes giving LINCS
warning on the same atoms but does it later.
Do you advice to keep reducing the time step in order to reach a
simulated
time where the pull of the whole molecule occurs and I see the force
peaking? I am still not sure why this happens...



No, I think the issue is probably more fundamental.  MARTINI uses fixed
secondary structure (bonds in the topology to preserve geometry).  You're
probably just pulling against those and the algorithms that work on
bonded
interactions are failing.

-Justin


Thanks.

Davide

On 7/02/13 1:05 PM, "Justin Lemkul"  wrote:




On 2/7/13 5:20 AM, Davide Mercadante wrote:

Dear All,

I am trying to run a pulling simulation on a small protein (18 aa)
using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions NA+ and CL-.

After the equilibration I start a constant velocity pulling along the
z-direction of the last atom of the chain while the first atom is
positionally restrained in xyz (basically I am stretching the
protein).
At some point from the start of the pulling simulation and before
reaching the full extension of the chain (force profile is still
steadily increasing without peaking) the simulation crashes giving me
these LINCS warnings:

Step 293252, time 5865.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.157274, max 0.291135 (between atoms 10 and 11)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length

Step 293252, time 5865.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.128562, max 0.230219 (between atoms 7 and 8)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.413291, max 0.828515 (between atoms 7 and 8)

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.587032, max 0.986890 (between atoms 11 and 13)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 7  8   46.60.2686   0.0579  0.3500
10 11  121.30.2481   0.0550  0.3500
13 15  168.50.2851   0.0278  0.3500

Step 293253, time 5865.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.108373, max 0.322423 (between atoms 19 and 21)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 7  8   45.00.2686   0.0600  0.3500
10 11   88.10.2481   0.0497  0.3500
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.330732, max 0.654588 (between atoms 23 and 25)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
21 23   42.00.2905   0.1426  0.3500
17 18   92.90.3146   0.1560  0.3000
15 17   35.30.5839   0.4003  0.3500
13 15  141.60.0278   0.2742  0.3500

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.312540, max 0.87 (between atoms 19 and 21)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
 8  9   48.00.3406   0.1435  0.3100
 7  8   82.30.0579   0.4596  0.3500
10 11  102.90.0550   0.5130  0.3500
11 12   51.90.5425   0.3643  0.4000
11 13   38.50.6954   0.1898  0.3500
13 15  143.40.0278   0.2879  0.3500
15 17   37.30.5839   0.3730  0.3500

Step 293254, time 5865.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.343084, max 0.751867 (between atoms 3 and 5)
17 18   93.20.3146   0.1563  0.3000
21 23   41.60.2905   0.1443  0.3500
23 24   33.00.3784   0.4007  0.4000
11 13   58.20.6954   0.3283  0.3500
 

Re: [gmx-users] Re: Re: Translating my system using editconf causes my run to crash!

[Justin Lemkul]

On 2/7/13 2:56 PM, S. Alireza Bagherzadeh wrote:

Dear Justin,

Today's Topics:


1. Re: Translating my system using editconf causes my runto
   crash! (Justin Lemkul)


--

Message: 1
Date: Wed, 06 Feb 2013 20:54:01 -0500
From: Justin Lemkul 
Subject: Re: [gmx-users] Translating my system using editconf causes
 my run  to crash!
To: Discussion list for GROMACS users 
Message-ID: <51130939.2090...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 2/6/13 3:03 PM, S. Alireza Bagherzadeh wrote:

Dear Mark,





Today's Topics:


 4. Translating my system using editconf causes my run to crash!
(S. Alireza Bagherzadeh)
 5. Re: Translating my system using editconf causes my run to
crash! (Mark Abraham)



--


Message: 5
Date: Tue, 5 Feb 2013 22:21:05 +0100
From: Mark Abraham 
Subject: Re: [gmx-users] Translating my system using editconf causes
  my run to   crash!
To: Discussion list for GROMACS users 
Message-ID:
  
Content-Type: text/plain; charset=ISO-8859-1

On Tue, Feb 5, 2013 at 10:05 PM, S. Alireza Bagherzadeh <
s.a.bagherzade...@gmail.com> wrote:


Hi everyone,

I am using "editconf" to translate my system along the z-axis.



Why? mdrun doesn't care.



Because I want to preserve the geometry of my system for the purpose of
visualization as well as some post-analysis code that I write.
I noticed that mdrun as an output gives an image of the simulation box

that

sits on the origin and extends along the positive direction of the
coordinate axises.

This might clarify what I mean:

My initial configuration looks like this:

GAS | WATER | ICE | WATER | GAS   (center of system at z-axis: z = 35
nm)

My final configuration looks like this:

TER | ICE | WATER | GAS GAS | WA(center of system at z-axis: z =
dZ/2 = 14.32431)

dZ is the simulation box length along the z-axis.



This all looks like a rather normal product of PBC.  It sounds like you're
just
repositioning the elements within the unit cell for visualization and
post-processing; where does a new simulation come into play?



There is no new simulation!

My primary question is about why translation causes a simulation to crash!
This looks so strange and weird to me.



OK, then this is a very different question.  Your original post seemed to 
indicate that you were translating coordinates and doing so caused the 
simulation to crash.  In contrast, what is actually happening is that the 
simulation is crashing because it is moving in a manner you believe to be 
incorrect, and you are simply post-processing the result to try to see what's 
going on.  Is all of this correct?  We need to be clear and on the same page to 
be productive.



With regards to the above, I understand that this is the product of PBC but
I was not able to convert (TER | ICE | WATER | GAS GAS | WA) to my original
set up (GAS | WATER | ICE | WATER | GAS) using trjconv along with -pbc
option.



Please post a full .mdp file.  Without it, there are too many things to guess 
at.

-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] problems for GPU simulations

[Szilárd Páll]

Hi,

If you have two GTX 590-s four devices should show up in nvidia-smi and
mdrun should also show four devices detected. As nvidia-smi shows only two
GPUs means that one of your cards is not functioning properly.

You can try to check what GPU devices does you operating system "see"
independently form the driver using the lspci command, e.g:
lspci | grep -i ".*VGA.*NVIDIA.*"

If you see two PCI devices in this output that means that both cards are
detected by the operating system. If nvidia-smi does not show all four
GPUs, there must be something wrong with your driver.

Cheers,

--
Szilárd


On Thu, Feb 7, 2013 at 5:08 PM, Albert  wrote:

> On 02/07/2013 01:34 PM, Szilárd Páll wrote:
>
>> Please make sure that nvididia-smi or the deviceQuery SDK tool show all
>> four GPUs. If that is the case and mdrun still shows only two, please file
>> a bug report with you OS info and a log file attached.
>>
>> Cheers,
>> --
>> Szilárd
>>
>
> no, it showed two. I don't know why it only work in beta version it can
> recognize 4 GPU, but in final version only 2 The fact is that the beta
> version use -np 4 can get double speed. The GTX590 have two core, so two
> GPU have 4 core.
>
>
> here is the log for nvidia-sim:
>
> Thu Feb  7 17:27:10 2013
> +-**-+
> | NVIDIA-SMI 2.285.05   Driver Version: 285.05.33 |
> |-**--+--+**
> --+
> | Nb.  Name | Bus IdDisp.  | Volatile ECC SB /
> DB |
> | Fan   Temp   Power Usage /Cap | Memory Usage | GPU Util. Compute
> M. |
> |=**==+==+**
> ==|
> | 0.  GeForce GTX 590   | :0C:00.0  N/A| N/AN/A |
> |   0%   55 C  N/A   N/A /  N/A |  22%  336MB / 1535MB |  N/A Default|
> |-**--+--+**
> --|
> | 1.  GeForce GTX 590   | :0B:00.0  N/A| N/AN/A |
> |  43%   57 C  N/A   N/A /  N/A |   0%5MB / 1535MB |  N/A Default|
> |-**--+--+**
> --|
> | Compute processes: GPU Memory |
> |  GPU  PID Process name Usage  |
> |=**==**
> ==|
> |  0.   ERROR: Not Supported
>|
> |  1.   ERROR: Not Supported
>|
> +-**--**
> --+
>
>
>
>
> here is the log for mdrun:
>
>
> Program mdrun_mpi, VERSION 4.6
> Source code file: /home/albert/Documents/2013-**
> 02-06/gromacs-4.6/src/gmxlib/**gmx_detect_hardware.c, line: 356
>
> Fatal error:
> Incorrect launch configuration: mismatching number of PP MPI processes and
> GPUs per node.
> mdrun_mpi was started with 4 PP MPI processes per node, but only 2 GPUs
> were detected.
> For more information and tips for troubleshooting, please check the GROMACS
> website at 
> http://www.gromacs.org/**Documentation/Errors
> --**-
>
> "I Like You. I Will Kill You Last" (Tyler in Fishtank)
>
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 0 out of 4
>
>
> --
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[gmx-users] calculate the size of protein

[Kieu Thu Nguyen]

Dear all,

I want to calculate the size of the protein. Which tool should i use for
this purpose ?

Thanks and regards,
KT
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Re: [gmx-users] Many energygrps to output

[Bogdan Costescu]

On Thu, Feb 7, 2013 at 8:13 PM, Yun Shi  wrote:
> So instead of making an index file with 399 groups of each residue in
> A and typing in rerun.mdp file 400 group names as
> "energygrps = A1 A2 A3 A4 ... A399 B", and issuing g_energy command 399 times,

There can be maximum 256 groups defined at once (Chapter 3.3 in
manual), so you can't do this anyway...

Cheers,
Bogdan
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Re: [gmx-users] Many energygrps to output

[Yun Shi]

I guess I will do mdrun -rerun 400 times then.

Thanks,
Yun

On Thu, Feb 7, 2013 at 9:06 PM, Bogdan Costescu  wrote:
> On Thu, Feb 7, 2013 at 8:13 PM, Yun Shi  wrote:
>> So instead of making an index file with 399 groups of each residue in
>> A and typing in rerun.mdp file 400 group names as
>> "energygrps = A1 A2 A3 A4 ... A399 B", and issuing g_energy command 399 
>> times,
>
> There can be maximum 256 groups defined at once (Chapter 3.3 in
> manual), so you can't do this anyway...
>
> Cheers,
> Bogdan
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Re: [gmx-users] calculate the size of protein

[Tsjerk Wassenaar]

Hi KT,

What do you mean with size?

- circumscribed radius: editconf
- radius of gyration: g_gyrate
- dimensions of fitting box: editconf
- volume: g_sas

Cheers,

Tsjerk

On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen wrote:

> Dear all,
>
> I want to calculate the size of the protein. Which tool should i use for
> this purpose ?
>
> Thanks and regards,
> KT
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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Re: [gmx-users] calculate the size of protein

[Kieu Thu Nguyen]

Thank Tsjerk ! I mean that i want to determine the dimensions (x, y, z) of
the protein


On Fri, Feb 8, 2013 at 1:48 PM, Tsjerk Wassenaar  wrote:

> Hi KT,
>
> What do you mean with size?
>
> - circumscribed radius: editconf
> - radius of gyration: g_gyrate
> - dimensions of fitting box: editconf
> - volume: g_sas
>
> Cheers,
>
> Tsjerk
>
> On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen  >wrote:
>
> > Dear all,
> >
> > I want to calculate the size of the protein. Which tool should i use for
> > this purpose ?
> >
> > Thanks and regards,
> > KT
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Re: Re: Error- Simulation box resizes during mdrun

[Bharath K. Srikanth]

Justin,

You're right, the density of the box does increase during the simulation.
But I don't believe the water is particularly sparse, since I've never
encountered this issue in previous simulations, when I used these
parameters for genbox while inserting water. The system density also
appears to have an acceptable value in the beginning.

Is there any other way I can approach this, for example, is there a
command/md.mdp option that would fix the size of my simulation box to the
initial values?

Cheers,
Bharath

> 3) I then re-inserted the peptide by editing the coordinate file, and ran
> an energy minimization. Then I added water using genbox, and ran another
> EM.
>
> 4) Then I ran the simulation for 3,000,000 steps (90 ns). While this was
> happening, I observed that the size of the box was beginning to change, in
> the z direction (not in the y direction as I said yesterday, but still,
> parallel to the plane of the bilayer).
>
> I've included some pictures here (in the .tga format), from before and
> after the simulation. When I ran it in vmd using the initial coordinates
> and the trajectory file, I could actually see the box resizing during the
> run.
>
> https://www.dropbox.com/l/UJuFbDTPaISIpkSf
>
> I'm sure there's a very simple explanation, but I can't seem to figure it
> out.
>

It's hard to tell from the way things are rendered, but it seems to me
that your
water is very diffuse, and over the course of the simulation, the density
of the
system is increasing to try to fill a lot of void space.  A simple
analysis of
density should show this rather clearly.





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