Re: [gmx-users] Normal Mode Analysis -- Expected Output

[Bryan Roessler]

My problem was here:

>nsteps  = 10
which should read
nsteps  = 1

I was under the assumption that the step numbers would correspond to the
number of calculated eigenvectors. All eigenvectors are calculated in step
1.

Thanks,

Bryan


On Thu, Apr 11, 2013 at 12:33 PM, David van der Spoel
wrote:

> On 2013-04-11 17:57, Bryan Roessler wrote:
>
>> Hello,
>>
>> I am running a normal mode analysis on a ~1500AA protein with the
>> following
>> mdp parameters:
>>
>> Log file opened on Tue Apr  9 09:55:00 2013
>> Host: uv1  pid: 128985  nodeid: 0  nnodes:  64
>> Gromacs version:VERSION 4.6.1
>> Precision:  double
>> Memory model:   64 bit
>> MPI library:MPI
>> OpenMP support: disabled
>> GPU support:disabled
>> invsqrt routine:gmx_software_invsqrt(x)
>> CPU acceleration:   AVX_256
>> FFT library:fftw-3.3.2-sse2
>> Large file support: enabled
>> RDTSCP usage:   enabled
>> Built on:   Fri Mar 15 09:20:59 CDT 2013
>> Built by:   asndcy@uv [CMAKE]
>> Build OS/arch:  Linux 3.0.58-0.6.6-default x86_64
>> Build CPU vendor:   GenuineIntel
>> Build CPU brand:Intel(R) Xeon(R) CPU E5-2667 0 @ 2.90GHz
>> Build CPU family:   6   Model: 45   Stepping: 7
>> Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
>> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
>> sse4.2 ssse3 tdt x2apic
>> C compiler: /opt/sgi/mpt/mpt-2.07/bin/**mpicc GNU gcc (GCC) 4.7.2
>> C compiler flags:   -mavx   -Wextra -Wno-missing-field-**initializers
>> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
>> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
>> -DNDEBUG
>>
>>
>>   :-)  G  R  O  M  A  C  S  (-:
>>
>> Good gRace! Old Maple Actually Chews Slate
>>
>>  :-)  VERSION 4.6.1  (-:
>>
>>  Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
>> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
>>
>>   Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph
>> Junghans,
>>  Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>>  Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>
>> Berk Hess, David van der Spoel, and Erik Lindahl.
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>   Copyright (c) 2001-2012,2013, The GROMACS development team at
>>  Uppsala University & The Royal Institute of Technology, Sweden.
>>  check out http://www.gromacs.org for more information.
>>
>>   This program is free software; you can redistribute it and/or
>> modify it under the terms of the GNU Lesser General Public License
>>  as published by the Free Software Foundation; either version 2.1
>>   of the License, or (at your option) any later version.
>>
>>  :-)  /opt/asn/apps/gromacs_4.6.1/**bin/mdrun_mpi_d (double
>> precision)  (-:
>>
>>
>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
>> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
>> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
>> molecular simulation
>> J. Chem. Theory Comput. 4 (2008) pp. 435-447
>>   --- Thank You ---  
>>
>>
>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
>> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J.
>> C.
>> Berendsen
>> GROMACS: Fast, Flexible and Free
>> J. Comp. Chem. 26 (2005) pp. 1701-1719
>>   --- Thank You ---  
>>
>>
>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
>> E. Lindahl and B. Hess and D. van der Spoel
>> GROMACS 3.0: A package for molecular simulation and trajectory analysis
>> J. Mol. Mod. 7 (2001) pp. 306-317
>>   --- Thank You ---  
>>
>>
>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
>> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
>> GROMACS: A message-passing parallel molecular dynamics implementation
>> Comp. Phys. Comm. 91 (1995) pp. 43-56
>>   --- Thank You ---  
>>
>>
>> Changing rlist from 1.47 to 1.4 for non-bonded 4x4 atom kernels
>>
>> Input Parameters:
>> integrator   = nm
>> nsteps   = 10
>> init-step= 0
>> cutoff-scheme= Verlet
>> ns_type  = Grid
>> nstlist  = 10
>> ndelta   = 2
>> nstcomm  = 100
>> comm-mode= Linear
>> nstlog   = 1000
>> nstxout  = 500
>> nstvout  = 500
>> nstfout  = 500
>> nstcalcenergy= 100
>> nstenergy= 500
>> nstxtcout= 0
>> init-t 

Re: [gmx-users] Normal Mode Analysis -- Expected Output

[David van der Spoel]

On 2013-04-11 17:57, Bryan Roessler wrote:

Hello,

I am running a normal mode analysis on a ~1500AA protein with the following
mdp parameters:

Log file opened on Tue Apr  9 09:55:00 2013
Host: uv1  pid: 128985  nodeid: 0  nnodes:  64
Gromacs version:VERSION 4.6.1
Precision:  double
Memory model:   64 bit
MPI library:MPI
OpenMP support: disabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Fri Mar 15 09:20:59 CDT 2013
Built by:   asndcy@uv [CMAKE]
Build OS/arch:  Linux 3.0.58-0.6.6-default x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2667 0 @ 2.90GHz
Build CPU family:   6   Model: 45   Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler: /opt/sgi/mpt/mpt-2.07/bin/mpicc GNU gcc (GCC) 4.7.2
C compiler flags:   -mavx   -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
-DNDEBUG


  :-)  G  R  O  M  A  C  S  (-:

Good gRace! Old Maple Actually Chews Slate

 :-)  VERSION 4.6.1  (-:

 Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
  Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
 Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

Berk Hess, David van der Spoel, and Erik Lindahl.

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  Copyright (c) 2001-2012,2013, The GROMACS development team at
 Uppsala University & The Royal Institute of Technology, Sweden.
 check out http://www.gromacs.org for more information.

  This program is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
 as published by the Free Software Foundation; either version 2.1
  of the License, or (at your option) any later version.

 :-)  /opt/asn/apps/gromacs_4.6.1/bin/mdrun_mpi_d (double precision)  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  


Changing rlist from 1.47 to 1.4 for non-bonded 4x4 atom kernels

Input Parameters:
integrator   = nm
nsteps   = 10
init-step= 0
cutoff-scheme= Verlet
ns_type  = Grid
nstlist  = 10
ndelta   = 2
nstcomm  = 100
comm-mode= Linear
nstlog   = 1000
nstxout  = 500
nstvout  = 500
nstfout  = 500
nstcalcenergy= 100
nstenergy= 500
nstxtcout= 0
init-t   = 0
delta-t  = 0.002
xtcprec  = 1000
fourierspacing   = 0.12
nkx  = 160
nky  = 160
nkz  = 216
pme-order= 4
ewald-rtol   = 1e-05
ewald-geometry   = 0
epsilon-surface  = 0
optimize-fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc  = No
bPrintNHChains   = FALSE
nsttcouple   = -1
epc  = No
epctype  = Isotropic

[gmx-users] Normal Mode Analysis -- Expected Output

[Bryan Roessler]

Hello,

I am running a normal mode analysis on a ~1500AA protein with the following
mdp parameters:

Log file opened on Tue Apr  9 09:55:00 2013
Host: uv1  pid: 128985  nodeid: 0  nnodes:  64
Gromacs version:VERSION 4.6.1
Precision:  double
Memory model:   64 bit
MPI library:MPI
OpenMP support: disabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Fri Mar 15 09:20:59 CDT 2013
Built by:   asndcy@uv [CMAKE]
Build OS/arch:  Linux 3.0.58-0.6.6-default x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2667 0 @ 2.90GHz
Build CPU family:   6   Model: 45   Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler: /opt/sgi/mpt/mpt-2.07/bin/mpicc GNU gcc (GCC) 4.7.2
C compiler flags:   -mavx   -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
-DNDEBUG


 :-)  G  R  O  M  A  C  S  (-:

   Good gRace! Old Maple Actually Chews Slate

:-)  VERSION 4.6.1  (-:

Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
   Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
 Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
 of the License, or (at your option) any later version.

:-)  /opt/asn/apps/gromacs_4.6.1/bin/mdrun_mpi_d (double precision)  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  


Changing rlist from 1.47 to 1.4 for non-bonded 4x4 atom kernels

Input Parameters:
   integrator   = nm
   nsteps   = 10
   init-step= 0
   cutoff-scheme= Verlet
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 100
   comm-mode= Linear
   nstlog   = 1000
   nstxout  = 500
   nstvout  = 500
   nstfout  = 500
   nstcalcenergy= 100
   nstenergy= 500
   nstxtcout= 0
   init-t   = 0
   delta-t  = 0.002
   xtcprec  = 1000
   fourierspacing   = 0.12
   nkx  = 160
   nky  = 160
   nkz  = 216
   pme-order= 4
   ewald-rtol   = 1e-05
   ewald-geometry   = 0
   epsilon-surface  = 0
   optimize-fft = TRUE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = No
   bPrintNHChains   = FALSE
   nsttcouple   = -1
   epc  = No
   epctype  = Isotropic
   nstpcouple   = -1
   tau-p= 1
   ref-p (3x3):
  ref-p[0]={ 1.0

Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges

[Mark Abraham]

On 12/21/2011 12:57 AM, Thomas Evangelidis wrote:

Mark, thanks for the prompt response!


I have done Normal Mode Analysis and have calculated partial
charges and the optimized geometry of a few compounds using
high-level QM calculations. Now I want to see (if possible) how
well GROMACS can reproduce the normal modes if I start from the
same optimized geometry and use the same partial charges.


In general for NMA to make sense you need to be at a stationary
point w.r.t. the atomic degrees of freedom of the model being
used. That won't be quite true at a QM geometry, so there's a
sense of apples-vs-oranges comparison.

If I get it right you mean that NMA in GROMACS must start from an 
energy minimum (stationary point) w.r.t the ff used (GAFF in my case), 
which means that an energy minimization is neccessary ever if I use an 
QM optimum geometry and the respective partial charges. Namely there 
is no way to reproduce the normal modes I obtained from QM 
calculations, correct?


You can choose to compare the two models on the same configuration, or 
at the local minimum w.r.t. each model that is nearest some 
configuration. Each approach has a minor flaw. How you need to manage 
precision varies with the choice you make.





An obvious problem is that the starting compound geometry is not
in full precision

The starting geometry is in full precision if it's the same as
that used for the QM calculation. That is quite possible to
achieve with .pdb or .gro input.

The same as the starting geometry or as the optimized geometry?


Your choice - your original workflow did no EM in GROMACS, so the use of 
.trr format was immaterial.



as highlighted in the documentation:

http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

Is it possible to create a full precision .trr coordinate file
from a .gro or any other structure file with modified 8-decimal
point coordinates?


I think you are misunderstanding the use of the word "precision"
here. In general, the same configuration will be represented
differently in .trr and .gro formats, with the former being a
closer approximation. Accordingly, one will get a different result
for NMA on the endpoint of GROMACS EM as observed in the .trr file
and as observed in the .gro file. The former will be closer to the
stationary point, and so lead to more acceptable estimates of the
normal modes. However, here you want to do NMA on the same
coordinates with two programs, so it is up to you to represent the
coordinates in a way that the two programs can compute on the same
approximation to the coordinates of the stationary point. There's
no need to convert to .trr (or the QM binary format), because all
that does is treat 2.613 as 2.613.


So a command line like this will do the job, right?

grompp_d4.5.5 -f nm.mdp -c ${ligand}_8_decimal_points.gro -p 
${ligand}.top -o nm.tpr


That copies the configuration in -c in the full precision available from 
the format of -c into the .tpr.


Mark

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Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges

[Thomas Evangelidis]

Mark, thanks for the prompt response!

I have done Normal Mode Analysis and have calculated partial charges and
> the optimized geometry of a few compounds using high-level QM calculations.
> Now I want to see (if possible) how well GROMACS can reproduce the normal
> modes if I start from the same optimized geometry and use the same partial
> charges.
>
>
> In general for NMA to make sense you need to be at a stationary point
> w.r.t. the atomic degrees of freedom of the model being used. That won't be
> quite true at a QM geometry, so there's a sense of apples-vs-oranges
> comparison.
>
>
If I get it right you mean that NMA in GROMACS must start from an energy
minimum (stationary point) w.r.t the ff used (GAFF in my case), which means
that an energy minimization is neccessary ever if I use an QM optimum
geometry and the respective partial charges. Namely there is no way to
reproduce the normal modes I obtained from QM calculations, correct?


> An obvious problem is that the starting compound geometry is not in full
> precision
>
> The starting geometry is in full precision if it's the same as that used
> for the QM calculation. That is quite possible to achieve with .pdb or .gro
> input.
>
>
The same as the starting geometry or as the optimized geometry?


> as highlighted in the documentation:
>
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
>
> Is it possible to create a full precision .trr coordinate file from a .gro
> or any other structure file with modified 8-decimal point coordinates?
>
>
> I think you are misunderstanding the use of the word "precision" here. In
> general, the same configuration will be represented differently in .trr and
> .gro formats, with the former being a closer approximation. Accordingly,
> one will get a different result for NMA on the endpoint of GROMACS EM as
> observed in the .trr file and as observed in the .gro file. The former will
> be closer to the stationary point, and so lead to more acceptable estimates
> of the normal modes. However, here you want to do NMA on the same
> coordinates with two programs, so it is up to you to represent the
> coordinates in a way that the two programs can compute on the same
> approximation to the coordinates of the stationary point. There's no need
> to convert to .trr (or the QM binary format), because all that does is
> treat 2.613 as 2.613.
>
>
So a command line like this will do the job, right?

grompp_d4.5.5 -f nm.mdp -c ${ligand}_8_decimal_points.gro -p ${ligand}.top
-o nm.tpr



Thomas





==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges

[Mark Abraham]

On 20/12/11, Thomas Evangelidis   wrote:
> Dear GROMACS users,
> 
> 
> I have done Normal Mode Analysis and have calculated partial charges and the 
> optimized geometry of a few compounds using high-level QM calculations. Now I 
> want to see (if possible) how well GROMACS can reproduce the normal modes if 
> I start from the same optimized geometry and use the same partial charges.
> 


In general for NMA to make sense you need to be at a stationary point w.r.t. 
the atomic degrees of freedom of the model being used. That won't be quite true 
at a QM geometry, so there's a sense of apples-vs-oranges comparison.
 

>  The command lines I use are the following:
> 
> 
> ligand="10058_F4.nw.new_GMX"
> 
> ## do Normal Mode Analysis
> grompp_d4.5.5 -f nm.mdp -c ${ligand}.gro -p ${ligand}.top -o nm.tpr
> mdrun_d4.5.5 -v -deffnm nm
> 
> ## calculate the eigenvectors/values of the Hessian matrix and write the 
> eigenvectors to a trajectory file
> 
> g_nmeig_d4.5.5 -f nm.mtx -s nm.tpr -of -ol -v -m -last 81
> 
> ## plot the vector components and the RMS fluctuation per atom of 
> eigenvectors for all eigenvectors
> echo 0 | g_anaeig_d4.5.5 -v eigenvec.trr -s nm.tpr -eig eigenval.xvg -comp 
> -rmsf -last -1
> 
> 
> ## create a trajectory from the eigenvector 76 (the first 6 are the rotation 
> and translation) to visualize the vibrations in VMD
> g_nmtraj_d4.5.5 -s nm.tpr -v eigenvec.trr -eignr "76" -nframes 10 -amplitude 
> 1 -o
> 
> 
> Most of the resulting normal modes do not coincide with the respective ones 
> calculated through QM. Does the order of the above command lines make sense?
> 
> 
> An obvious problem is that the starting compound geometry is not in full 
> precision
> 


The starting geometry is in full precision if it's the same as that used for 
the QM calculation. That is quite possible to achieve with .pdb or .gro input.
 

>  as highlighted in the documentation:
> 
> 
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
> 
> Is it possible to create a full precision .trr coordinate file from a .gro or 
> any other structure file with modified 8-decimal point coordinates?
> 


I think you are misunderstanding the use of the word "precision" here. In 
general, the same configuration will be represented differently in .trr and 
.gro formats, with the former being a closer approximation. Accordingly, one 
will get a different result for NMA on the endpoint of GROMACS EM as observed 
in the .trr file and as observed in the .gro file. The former will be closer to 
the stationary point, and so lead to more acceptable estimates of the normal 
modes. However, here you want to do NMA on the same coordinates with two 
programs, so it is up to you to represent the coordinates in a way that the two 
programs can compute on the same approximation to the coordinates of the 
stationary point. There's no need to convert to .trr (or the QM binary format), 
because all that does is treat 2.613 as 2.613.


Mark
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[gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges

[Thomas Evangelidis]

Dear GROMACS users,


I have done Normal Mode Analysis and have calculated partial charges and
the optimized geometry of a few compounds using high-level QM calculations.
Now I want to see (if possible) how well GROMACS can reproduce the normal
modes if I start from the same optimized geometry and use the same partial
charges. The command lines I use are the following:

ligand="10058_F4.nw.new_GMX"

## do Normal Mode Analysis
grompp_d4.5.5 -f nm.mdp -c ${ligand}.gro -p ${ligand}.top -o nm.tpr
mdrun_d4.5.5 -v -deffnm nm

## calculate the eigenvectors/values of the Hessian matrix and write the
eigenvectors to a trajectory file
g_nmeig_d4.5.5 -f nm.mtx -s nm.tpr -of -ol -v -m -last 81

## plot the vector components and the RMS fluctuation per atom of
eigenvectors for all eigenvectors
echo 0 | g_anaeig_d4.5.5 -v eigenvec.trr -s nm.tpr -eig eigenval.xvg -comp
-rmsf -last -1

## create a trajectory from the eigenvector 76 (the first 6 are the
rotation and translation) to visualize the vibrations in VMD
g_nmtraj_d4.5.5 -s nm.tpr -v eigenvec.trr -eignr "76" -nframes 10
-amplitude 1 -o

Most of the resulting normal modes do not coincide with the respective ones
calculated through QM. Does the order of the above command lines make sense?


An obvious problem is that the starting compound geometry is not in full
precision as highlighted in the documentation:

http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

Is it possible to create a full precision .trr coordinate file from a .gro
or any other structure file with modified 8-decimal point coordinates?


I am looking forward for an answer,
Thomas
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Re: [gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

Hi James,

PCA on a trajectory is about fluctuations -the correlation between
deviations from an average positions-, NMA is about penalized
displacement -the increase in potential energy due to concurrent
displacement-. In NMA the lowest mode is that for which most atoms can
move most unrestrictedly. It seems evident that the side chains will
severely penalize the displacement of c-alpha atoms. I wouldn't call
that a solvent effect or damping. It's the nature of the protein, and
the error you make in your model when restricting to c-alpha atoms
only.

With respect to the other question, I think the best I can do is to
urge you to read more on principal component analysis, until you
understand the meaning of 'principal component', 'eigenvalue',
'score', 'projection' and 'loading' :)

Cheers,

Tsjerk

On Thu, Nov 10, 2011 at 8:51 AM, James Starlight  wrote:
> Hi Tsjerk,
>
> Thanks for help. So as I understood if I want to calculate fluctuations only
> for Calpha I must first to do NMA of my reference in some mode subspace
> consisted of the eigenvectors for Calpha atoms only. Does this correct ?
> Previously I've done something like this for random subspace of modes in
> MMTK (just to reduce the space for calculation) but how perform such
> operation in Gromacs I havent known yet :)
>
>
>> The c-alphas are less hindered in the second model due to the absence
>> of the side chains and such. There's just more freedom.
>>
>
> It's known that solevnt for instance could significant damp motions from
> normal modes. So in my case It seems that sidechains act as the solvent. How
> do you think may sidechains not only damp motions oberved for C-alpha atoms
> merely but also change the trajectory of their motion?
>
>
> James
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

Hi Tsjerk,

Thanks for help. So as I understood if I want to calculate fluctuations
only for Calpha I must first to do NMA of my reference in some mode
subspace consisted of the eigenvectors for Calpha atoms only. Does this
correct ?
Previously I've done something like this for random subspace of modes in
MMTK (just to reduce the space for calculation) but how perform such
operation in Gromacs I havent known yet :)


The c-alphas are less hindered in the second model due to the absence
> of the side chains and such. There's just more freedom.
>
>
It's known that solevnt for instance could significant damp motions from
normal modes. So in my case It seems that sidechains act as the solvent.
How do you think may sidechains not only damp motions oberved for C-alpha
atoms merely but also change the trajectory of their motion?


James
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Re: [gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

Hi James,

> 1- Can I obtain same fluctuations along ensemble of several modes (i.e
> averaged fluctuations along modes from n to k ) in one graph ?

The total fluctuation is the sum of the fluctuations along all the
modes. To get what you want, you just need to some the fluctuations.
Alternatively, you can filter a trajectory using a set of modes and do
further analysis on that.

> 2- Is there any way to obtain fluctuations of C-alpha atoms or backbone only
> from full atomic model ?

See the answer above.

> but I can chose only full atomic representation of the system consisted of
> 6518 atoms and any other selection would produce error.
> Is there any other way to obtain fluctuations on reduced number of atoms
> from full-atomic system ?

g_anaeig needs the atoms to match with the eigenvectors, which pertain
to the full set of atoms.

> 3- Also I've done two different NMA from one reference ( for full atomic
> model and for C-alpha mode).
> The overal picture of RMSF for instance was overal in both of the analysis
> but in case of the C-alpha only ANM RMSF were bigger in 10 times (0.02 Nm in
> case of full atomic NMA vs 2 NM in case of C-alpha NMA on equat residues).
> Why that difference might occur? Is there any way to increase amplitude of
> fluctuations by the temperature rising for instance ?

The c-alphas are less hindered in the second model due to the absence
of the side chains and such. There's just more freedom.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

Mark hello,

2011/11/10 Mark Abraham 

> From your description, I think you're comparing apples with oranges.
>
>
I just want compare results of coarse grained NMA based on C-alpha only
with full atomic NMA.
I've already done that work and obtain that

1- overal picture of fluctuations is the same for both methods
2- in case of full atomic NMA overal motion is damped in comparison to the
C-alpha only NMA ( rmsf of fluctuations are greater in 10 times)

3 Finally I just want to obtain fluctuations on Calpha atoms only for my
full atomic NMA for better comparison with cg NMA (e.g representation on
one graph RMSF on Calpha atoms only for both methods  )

James


>
>  Is there any way to increase amplitude of fluctuations by the temperature
>> rising for instance ?
>>
>
>  NMA is athermal.
>
>
> Mark
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 10/11/2011 5:36 PM, James Starlight wrote:

Thank you, Mark.

By the way, also I have some question about data analysing

From g_anaeig  I can obtain atom fluctuations along defined mode



1- Can I obtain same fluctuations along ensemble of several modes (i.e 
averaged fluctuations along modes from n to k ) in one graph ?


Yes, through suitable use of your graphing program on multiple input 
files. IMO that would not be a suitable discussion for this list. 
Suggestions for graphing programs and some tricks of the trade are on 
the GROMACS webpage.




2- Is there any way to obtain fluctuations of C-alpha atoms or 
backbone only from full atomic model ?

E.g on start g_anaeig ask me

Select an index group of 6518 elements that corresponds to the 
eigenvectors

Group 0 ( System) has  6518 elements
Group 1 (Protein) has  6518 elements
Group 2 (  Protein-H) has  3269 elements
Group 3 (C-alpha) has   413 elements
Group 4 (   Backbone) has  1239 elements
...

but I can chose only full atomic representation of the system 
consisted of 6518 atoms and any other selection would produce error.
Is there any other way to obtain fluctuations on reduced number of 
atoms from full-atomic system ?


Unless g_nmeig can be persuaded to calculate on a subset of the Hessian, 
I would guess not.





3- Also I've done two different NMA from one reference ( for full 
atomic model and for C-alpha mode).
The overal picture of RMSF for instance was overal in both of the 
analysis but in case of the C-alpha only ANM RMSF were bigger in 10 
times (0.02 Nm in case of full atomic NMA vs 2 NM in case of C-alpha 
NMA on equat residues).

Why that difference might occur?


From your description, I think you're comparing apples with oranges.

Is there any way to increase amplitude of fluctuations by the 
temperature rising for instance ?


 NMA is athermal.

Mark
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

Thank you, Mark.

By the way, also I have some question about data analysing

>From g_anaeig  I can obtain atom fluctuations along defined mode



1- Can I obtain same fluctuations along ensemble of several modes (i.e
averaged fluctuations along modes from n to k ) in one graph ?

2- Is there any way to obtain fluctuations of C-alpha atoms or backbone
only from full atomic model ?
E.g on start g_anaeig ask me

Select an index group of 6518 elements that corresponds to the eigenvectors
Group 0 ( System) has  6518 elements
Group 1 (Protein) has  6518 elements
Group 2 (  Protein-H) has  3269 elements
Group 3 (C-alpha) has   413 elements
Group 4 (   Backbone) has  1239 elements
...

but I can chose only full atomic representation of the system consisted of
6518 atoms and any other selection would produce error.
Is there any other way to obtain fluctuations on reduced number of atoms
from full-atomic system ?


3- Also I've done two different NMA from one reference ( for full atomic
model and for C-alpha mode).
The overal picture of RMSF for instance was overal in both of the analysis
but in case of the C-alpha only ANM RMSF were bigger in 10 times (0.02 Nm
in case of full atomic NMA vs 2 NM in case of C-alpha NMA on equat
residues).
Why that difference might occur? Is there any way to increase amplitude of
fluctuations by the temperature rising for instance ?

Thanks,

James


2011/11/10 Mark Abraham 

> On 10/11/2011 6:48 AM, James Starlight wrote:
>
>> I've another question about NMA.
>>
>> 1- As I understood the Sparce matrix method is used on default in case
>> when my reference structure consist of alot of atoms. If this true the
>> output Hessian.mtx would be in sparce format, wouldn't it ?
>>
>>
>> 2- How I can convert output.mtx to the txt format ? As the consequence I
>> want to obtain something like this
>> http://www.csb.pitt.edu/prody/**_downloads/oanm_hes.txt
>>
>
> GROMACS is not very helpful with matrices of data, unfortunately. You can
> dump the numbers out of the .mtx format with gmxdump, but you would be on
> your own to then convert it to some other format you want (i.e. write some
> script).
>
> Mark
>
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 10/11/2011 6:48 AM, James Starlight wrote:

I've another question about NMA.

1- As I understood the Sparce matrix method is used on default in case 
when my reference structure consist of alot of atoms. If this true the 
output Hessian.mtx would be in sparce format, wouldn't it ?



2- How I can convert output.mtx to the txt format ? As the consequence 
I want to obtain something like this

http://www.csb.pitt.edu/prody/_downloads/oanm_hes.txt


GROMACS is not very helpful with matrices of data, unfortunately. You 
can dump the numbers out of the .mtx format with gmxdump, but you would 
be on your own to then convert it to some other format you want (i.e. 
write some script).


Mark
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

I've another question about NMA.

1- As I understood the Sparce matrix method is used on default in case when
my reference structure consist of alot of atoms. If this true the output
Hessian.mtx would be in sparce format, wouldn't it ?


2- How I can convert output.mtx to the txt format ? As the consequence I
want to obtain something like this
http://www.csb.pitt.edu/prody/_downloads/oanm_hes.txt
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Re: [gmx-users] Normal Mode Analysis

[Justin A. Lemkul]

James Starlight wrote:

Mark, hello!

I think that there is some error durins saving of my minimization data

As the result of the minimization I've obtained

(1)
Low-Memory BFGS Minimizer converged to machine precision in 3723 steps,
but did not reach the requested Fmax < 0.
Potential Energy  =  2.08789280994511e+03
Maximum force =  3.01715687185776e-04 on atom 58
Norm of force =  3.0930131065e-05

So the Fmax is sufficient low

But when I've load this data for NMA I've obtained

(2)
Maximum force: 8.41270e+02
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.


So the Fmax is indeed very big for NMA but why it's not the same as in 
the (1)?


This is my script for NMA wich indicate that I've load to NMA suitable data

# Steep
grompp_d -f minimSTEEP.mdp -c conf_newbox.gro -p topol.top -o minimizedS.tpr

mdrun_d -v -deffnm minimizedS


# Grad
grompp_d -f minimGRAD.mdp -c minimizedS.gro -p topol.top -o 
minimizedGRAD.tpr


mdrun_d -v -deffnm minimizedGRAD


# NMA
grompp_d -f nma.mdp -c minimizedGRAD.tpr -p topol.top -o fornma.tpr

mdrun_d -v -deffnm fornma -mtx nm.mtx




Where is the error?




You're using the unminimized coordinates as input into NMA.  The file 
"minimizedGRAD.tpr" contains the configuration before doing L-BFGS minimization, 
so it is not sufficiently minimized.


http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Normal Mode Analysis

[James Starlight]

Mark, hello!

I think that there is some error durins saving of my minimization data

As the result of the minimization I've obtained

(1)
Low-Memory BFGS Minimizer converged to machine precision in 3723 steps,
but did not reach the requested Fmax < 0.
Potential Energy  =  2.08789280994511e+03
Maximum force =  3.01715687185776e-04 on atom 58
Norm of force =  3.0930131065e-05

So the Fmax is sufficient low

But when I've load this data for NMA I've obtained

(2)
Maximum force: 8.41270e+02
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.


So the Fmax is indeed very big for NMA but why it's not the same as in the
(1)?

This is my script for NMA wich indicate that I've load to NMA suitable data

# Steep
grompp_d -f minimSTEEP.mdp -c conf_newbox.gro -p topol.top -o minimizedS.tpr

mdrun_d -v -deffnm minimizedS


# Grad
grompp_d -f minimGRAD.mdp -c minimizedS.gro -p topol.top -o
minimizedGRAD.tpr

mdrun_d -v -deffnm minimizedGRAD


# NMA
grompp_d -f nma.mdp -c minimizedGRAD.tpr -p topol.top -o fornma.tpr

mdrun_d -v -deffnm fornma -mtx nm.mtx




Where is the error?


James


2011/10/28 Mark Abraham 

>  On 28/10/2011 2:30 AM, James Starlight wrote:
>
> That's energy ouptut from minimization with that parametries ( there is
> also 1 step of steep minimization before that )
>
> integrator= l-bfgs
> emtol= 0.001
> emstep  = 0.001  ; Energy step size
> nsteps= 50  ; Maximum number of (minimization)
> steps to perform
>
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist= 1; Frequency to update the neighbor list and long
> range forces
> ns_type= grid; Method to determine neighbor list (simple,
> grid)
> rlist= 1.2; Cut-off for making neighbor list (short range
> forces)
> coulombtype= Shift
> rcoulomb= 1.0
> rcoulomb_switch= 0.7
> vdwtype = Shift
> rvdw= 1.0
> rvdw_switch = 0.7
>
>
> Output:
>
> Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 3646 steps
> Potential Energy  =  2.28946300988746e+03
> Maximum force =  8.47298141911052e-04 on atom 100
> Norm of force =  3.90346504086500e-04
>
> I'm not sure about the succses of that minimization due to the big Epot.
>
>
>
>
>  You look like you are shuffling deck chairs on the Titanic. I suggested
> you actually go and visualize your input and output trajectories. Sadly
> that doesn't seem to have happened.
>
> Mark
>
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 28/10/2011 2:30 AM, James Starlight wrote:
That's energy ouptut from minimization with that parametries ( there 
is also 1 step of steep minimization before that )


integrator= l-bfgs
emtol= 0.001
emstep  = 0.001  ; Energy step size
nsteps= 50  ; Maximum number of (minimization) 
steps to perform



; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions
nstlist= 1; Frequency to update the neighbor list and 
long range forces
ns_type= grid; Method to determine neighbor list 
(simple, grid)
rlist= 1.2; Cut-off for making neighbor list (short 
range forces)

coulombtype= Shift
rcoulomb= 1.0
rcoulomb_switch= 0.7
vdwtype = Shift
rvdw= 1.0
rvdw_switch = 0.7


Output:

Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 3646 steps
Potential Energy  =  2.28946300988746e+03
Maximum force =  8.47298141911052e-04 on atom 100
Norm of force =  3.90346504086500e-04

I'm not sure about the succses of that minimization due to the big Epot.




 You look like you are shuffling deck chairs on the Titanic. I 
suggested you actually go and visualize your input and output 
trajectories. Sadly that doesn't seem to have happened.


Mark
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

That's energy ouptut from minimization with that parametries ( there is also
1 step of steep minimization before that )

integrator= l-bfgs
emtol= 0.001
emstep  = 0.001  ; Energy step size
nsteps= 50  ; Maximum number of (minimization) steps
to perform


; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long
range forces
ns_type= grid; Method to determine neighbor list (simple,
grid)
rlist= 1.2; Cut-off for making neighbor list (short range
forces)
coulombtype= Shift
rcoulomb= 1.0
rcoulomb_switch= 0.7
vdwtype = Shift
rvdw= 1.0
rvdw_switch = 0.7


Output:

Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 3646 steps
Potential Energy  =  2.28946300988746e+03
Maximum force =  8.47298141911052e-04 on atom 100
Norm of force =  3.90346504086500e-04

I'm not sure about the succses of that minimization due to the big Epot.
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

I've used double precision. Today I'll copied output because it's done on
lab comp but from the output log I've found that minimization was not
completed ( e.g when I've calculate Normal Modes with that minimized
structure I've obtain message that my system was not minimized properly )

2011/10/26 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Justin,
>>
>>
>> I've forced with the problem that I could not prorerly minimized my system
>> in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot
>> value lower than +3.00 with that parametries ( I've used KALP peptide as a
>> test input )
>>
>>
> The Epot value is less significant than Fmax (which is what is set in the
> .mdp file, anyway).  What Fmax do you achieve?  Real copied and pasted
> output would be useful.
>
>
>  ; Parameters describing what to do, when to stop and what to save
>> integrator= steep   emtol= 1  ; Stop minimization when
>> the maximum force < 1.0 kJ/mol/nm
>> emstep  = 0.01  ; Energy step size
>> nsteps= 500  ; Maximum number of (minimization) steps
>> to perform
>>
>>
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist= 1; Frequency to update the neighbor list and long
>> range forces
>> ns_type= grid; Method to determine neighbor list (simple,
>> grid)
>> rlist= 1.2; Cut-off for making neighbor list (short range
>> forces)
>> coulombtype= Shift   rcoulomb= 1.0
>> rcoulomb_switch= 0.0
>> vdwtype = Shift
>> rvdw= 1.0
>> rvdw_switch = 0.0
>> Than I've tried to futher minimized this structure via  l-bfgs algorithm
>> by
>>
>> integrator= l-bfgs
>> dt  =  0.01
>> emtol= 0.001 ;
>> emstep  = 0.1  ; Energy step size
>> nsteps= 5000  ; Maximum number of (minimization) steps
>> to perform
>>
>> but Epot was still big.
>>
>> What I've done wrong ?
>>
>
> Are you using single- or double-precision?
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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] Normal Mode Analysis

[Justin A. Lemkul]

James Starlight wrote:

Justin,


I've forced with the problem that I could not prorerly minimized my 
system in the NMA conditions. Even in STEEP minimizaation I could not 
obtain Epot value lower than +3.00 with that parametries ( I've used 
KALP peptide as a test input )




The Epot value is less significant than Fmax (which is what is set in the .mdp 
file, anyway).  What Fmax do you achieve?  Real copied and pasted output would 
be useful.



; Parameters describing what to do, when to stop and what to save
integrator= steep   
emtol= 1  ; Stop minimization when the maximum force < 1.0 
kJ/mol/nm

emstep  = 0.01  ; Energy step size
nsteps= 500  ; Maximum number of (minimization) 
steps to perform




; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions
nstlist= 1; Frequency to update the neighbor list and 
long range forces
ns_type= grid; Method to determine neighbor list 
(simple, grid)
rlist= 1.2; Cut-off for making neighbor list (short 
range forces)
coulombtype= Shift   
rcoulomb= 1.0

rcoulomb_switch= 0.0
vdwtype = Shift
rvdw= 1.0
rvdw_switch = 0.0   


Than I've tried to futher minimized this structure via  l-bfgs algorithm by

integrator= l-bfgs
dt  =  0.01
emtol= 0.001 ;
emstep  = 0.1  ; Energy step size
nsteps= 5000  ; Maximum number of (minimization) 
steps to perform


but Epot was still big.

What I've done wrong ?


Are you using single- or double-precision?

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Normal Mode Analysis

[James Starlight]

Justin,


I've forced with the problem that I could not prorerly minimized my system
in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot
value lower than +3.00 with that parametries ( I've used KALP peptide as a
test input )

; Parameters describing what to do, when to stop and what to save
integrator= steep
emtol= 1  ; Stop minimization when the maximum force < 1.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 500  ; Maximum number of (minimization) steps to
perform



; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long
range forces
ns_type= grid; Method to determine neighbor list (simple,
grid)
rlist= 1.2; Cut-off for making neighbor list (short range
forces)
coulombtype= Shift
rcoulomb= 1.0
rcoulomb_switch= 0.0
vdwtype = Shift
rvdw= 1.0
rvdw_switch = 0.0

Than I've tried to futher minimized this structure via  l-bfgs algorithm by

integrator= l-bfgs
dt  =  0.01
emtol= 0.001 ;
emstep  = 0.1  ; Energy step size
nsteps= 5000  ; Maximum number of (minimization) steps
to perform

but Epot was still big.

What I've done wrong ?
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Re: [gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

Hi James,

Regarding PCA and NMA congruency, they are different things, unless
the energy landscape consists of a single harmonic potential well. The
principal components and the normal modes will usually correlate quite
well, but if the simulation is sampling different energy minima, there
may be quite a difference. You can easily work that out graphically
for a two dimensional energy landscape :)

Cheers,

Tsjerk

On Wed, Oct 26, 2011 at 2:57 PM, Justin A. Lemkul  wrote:
>
>
> James Starlight wrote:
>>
>> Mark,
>>
>> 2011/10/26 Mark Abraham > >
>>
>>
>>    Or that your starting structure is not close enough to a sensible
>>    minimum for a local gradient-based optimizer to do the job. Look at
>>    the atoms with the large forces and see what you can learn.
>>
>> So for that purpose I've done steep minimization first and only that based
>> on that minimized structure I did CG minimization. I changed the emtool (
>> from 100 to 1000) as well as step size but my structure always have not been
>> prorely minimized ( based on the system output ). Also I've found that there
>> is third L-BFGS 
>> algorithm for minimization. In what cases this minimization could be
>> helpfull?
>>
>
> You should probably be using it.
>
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
>
> Note that increasing emtol from 100 to 1000 actually makes your results
> worse, since mdrun will stop when the maximum force is below 1000 kJ/mol-nm,
> which is orders of magnitude too high for NMA.
>
> -Justin
>
>>
>>
>>    Sorry, we can't make guesses based on things you can't remember
>>    details about. Maybe you want to consider Essential Dynamics.
>>
>>
>> As I know the Essential dynamics is the type of the PC analysis ( in this
>> case the ensemble of the analysed structures is replaced by the ensemble of
>> the MD snapshots ). But I've heard that there is possible ways to extract
>> normal modes indirectly from the output trajectories.
>>
>>
>> James
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing list    gmx-users@gromacs.org
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Normal Mode Analysis

[Justin A. Lemkul]

James Starlight wrote:

Mark,

2011/10/26 Mark Abraham >



Or that your starting structure is not close enough to a sensible
minimum for a local gradient-based optimizer to do the job. Look at
the atoms with the large forces and see what you can learn.

So for that purpose I've done steep minimization first and only that 
based on that minimized structure I did CG minimization. I changed the 
emtool ( from 100 to 1000) as well as step size but my structure always 
have not been prorely minimized ( based on the system output ). Also 
I've found that there is third L-BFGS 
 algorithm for 
minimization. In what cases this minimization could be helpfull?




You should probably be using it.

http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

Note that increasing emtol from 100 to 1000 actually makes your results worse, 
since mdrun will stop when the maximum force is below 1000 kJ/mol-nm, which is 
orders of magnitude too high for NMA.


-Justin




Sorry, we can't make guesses based on things you can't remember
details about. Maybe you want to consider Essential Dynamics.


As I know the Essential dynamics is the type of the PC analysis ( in 
this case the ensemble of the analysed structures is replaced by the 
ensemble of the MD snapshots ). But I've heard that there is possible 
ways to extract normal modes indirectly from the output trajectories.



James



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Normal Mode Analysis

[James Starlight]

Mark,

2011/10/26 Mark Abraham 

>
>  Or that your starting structure is not close enough to a sensible minimum
> for a local gradient-based optimizer to do the job. Look at the atoms with
> the large forces and see what you can learn.
>
So for that purpose I've done steep minimization first and only that based
on that minimized structure I did CG minimization. I changed the emtool (
from 100 to 1000) as well as step size but my structure always have not been
prorely minimized ( based on the system output ). Also I've found that there
is third L-BFGS
algorithm for
minimization. In what cases this minimization could be
helpfull?



> Sorry, we can't make guesses based on things you can't remember details
> about. Maybe you want to consider Essential Dynamics.
>

As I know the Essential dynamics is the type of the PC analysis ( in this
case the ensemble of the analysed structures is replaced by the ensemble of
the MD snapshots ). But I've heard that there is possible ways to extract
normal modes indirectly from the output trajectories.


James
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 26/10/2011 11:04 PM, James Starlight wrote:

Mark hello,

2011/10/26 Mark Abraham >



We don't know the sense in which it "didn't minimize properly," so
there's not much point us guessing.


The output value for Epot was -2.0 after steep minimization and -2.5 
after CG. Also as the consequense after both energy minimization runs 
the system told me that the system have not been minimized completely 
or the step size was too short ( I've changd the step size from 0.01 
in both directions as well as EMtool from 1000 to 0.1 but that results 
were unchanged )


Also during diagonalization of the Hessian the system told me that 
lowest six modes were not zero's in their frequensies. It's also could 
indicate that I've analyzed not properly minimized structure


Or that your starting structure is not close enough to a sensible 
minimum for a local gradient-based optimizer to do the job. Look at the 
atoms with the large forces and see what you can learn.


By the way I've heard that there is possible way to extract Normal 
Modes from MD trajectories directly. E.g I've simulated my protein and 
obtain trr file and want to extract from that trajectory all 
eigenvectors ( modes) separately. Might it be realized in Gromacs and 
via what program should I do it?


Sorry, we can't make guesses based on things you can't remember details 
about. Maybe you want to consider Essential Dynamics.


Mark
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

Mark hello,

2011/10/26 Mark Abraham 

>
>  We don't know the sense in which it "didn't minimize properly," so there's
> not much point us guessing.
>
>
> The output value for Epot was -2.0 after steep minimization and -2.5 after
CG. Also as the consequense after both energy minimization runs the system
told me that the system have not been minimized completely or the step size
was too short ( I've changd the step size from 0.01 in both directions as
well as EMtool from 1000 to 0.1 but that results were unchanged )

Also during diagonalization of the Hessian the system told me that lowest
six modes were not zero's in their frequensies. It's also could indicate
that I've analyzed not properly minimized structure



By the way I've heard that there is possible way to extract Normal Modes
from MD trajectories directly. E.g I've simulated my protein and obtain trr
file and want to extract from that trajectory all eigenvectors ( modes)
separately. Might it be realized in Gromacs and via what program should I do
it?

James
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 26/10/2011 7:54 PM, James Starlight wrote:
I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm 
might provide good results.


But now I have some problems with minimization of my initial structure

Firstly, I've performed steep minimization ( emtool=1000,  emstep  
= 0.01 ) and than CG minimization (emtool=1,  emstep  = 0.001) but 
as the result I've obtain that my struucture didnt minimize properly.

Is there any different strategies for the minimization for the ANM ?


We don't know the sense in which it "didn't minimize properly," so 
there's not much point us guessing.




In addition I'd like to know about conditions of such normal mode 
simulations. Does this procedure require in the PBC ? ( I've performed 
all steps including energy minimization in vacuu)


Whether not PBC represents useful boundary conditions depends on what 
conditions you are trying to model - whether possible periodicity 
artefacts or boundary artefacts are more likely to affect your results.


It does sound like you would benefit from reading some good textbook 
material on molecular simulation :)


Mark




James

2011/10/25 Mark Abraham >


On 25/10/2011 3:30 AM, James Starlight wrote:

I understand this but I've not been able found such information.
I dont need in the most accurately  parametries for all cutt-offs
of my system but I want to gain inside into the basic cutt- offs
worked with the Normal mode analysis.


The cut-offs are particular to the force field, not the manner in
which the force field is used (EM vs MD vs whatever). There are
literature references in the GROMACS manual, and also in the
published work that you have been reading because it has
objectives similar to yours. (hint, hint)



E.g I've found that PME is not worked here. 


PME does work here. Last time you were apparently mis-matching
files...



So I must to constrain my system with simplest cuttoffs. Could
you provide me with the simple example e.g cutt of for
interaction beetwen C-alpha atoms only etc?


You can't do that, and shouldn't even if you could.

Mark




James



These are particular to the force field involved, not the
software. Please consult the appropriate literature, and see
what others have used for similar work.




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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm might
provide good results.

But now I have some problems with minimization of my initial structure

Firstly, I've performed steep minimization ( emtool=1000,  emstep  =
0.01 ) and than CG minimization (emtool=1,  emstep  = 0.001) but as the
result I've obtain that my struucture didnt minimize properly.
Is there any different strategies for the minimization for the ANM ?

In addition I'd like to know about conditions of such normal mode
simulations. Does this procedure require in the PBC ? ( I've performed all
steps including energy minimization in vacuu)


James

2011/10/25 Mark Abraham 

>  On 25/10/2011 3:30 AM, James Starlight wrote:
>
> I understand this but I've not been able found such information. I dont
> need in the most accurately  parametries for all cutt-offs of my system but
> I want to gain inside into the basic cutt- offs worked with the Normal mode
> analysis.
>
>
> The cut-offs are particular to the force field, not the manner in which the
> force field is used (EM vs MD vs whatever). There are literature references
> in the GROMACS manual, and also in the published work that you have been
> reading because it has objectives similar to yours. (hint, hint)
>
>
> E.g I've found that PME is not worked here.
>
>
> PME does work here. Last time you were apparently mis-matching files...
>
>
> So I must to constrain my system with simplest cuttoffs. Could you provide
> me with the simple example e.g cutt of for interaction beetwen C-alpha atoms
> only etc?
>
>
> You can't do that, and shouldn't even if you could.
>
> Mark
>
>
>
> James
>
>
>
>>  These are particular to the force field involved, not the software.
>> Please consult the appropriate literature, and see what others have used for
>> similar work.
>>
>>
>
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 25/10/2011 3:30 AM, James Starlight wrote:
I understand this but I've not been able found such information. I 
dont need in the most accurately  parametries for all cutt-offs of my 
system but I want to gain inside into the basic cutt- offs worked with 
the Normal mode analysis.


The cut-offs are particular to the force field, not the manner in which 
the force field is used (EM vs MD vs whatever). There are literature 
references in the GROMACS manual, and also in the published work that 
you have been reading because it has objectives similar to yours. (hint, 
hint)




E.g I've found that PME is not worked here. 


PME does work here. Last time you were apparently mis-matching files...

So I must to constrain my system with simplest cuttoffs. Could you 
provide me with the simple example e.g cutt of for interaction beetwen 
C-alpha atoms only etc?


You can't do that, and shouldn't even if you could.

Mark



James



These are particular to the force field involved, not the
software. Please consult the appropriate literature, and see what
others have used for similar work.



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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

I understand this but I've not been able found such information. I dont need
in the most accurately  parametries for all cutt-offs of my system but I
want to gain inside into the basic cutt- offs worked with the Normal mode
analysis.

E.g I've found that PME is not worked here. So I must to constrain my system
with simplest cuttoffs. Could you provide me with the simple example e.g
cutt of for interaction beetwen C-alpha atoms only etc?

James



> These are particular to the force field involved, not the software. Please
> consult the appropriate literature, and see what others have used for
> similar work.
>
>
>
>
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 24/10/2011 6:56 PM, James Starlight wrote:
As the consequence I've done my NMA calculations without of any 
constraints :)


integrator= nm; Normal Mode Analysis
constraints =  none


but I'm not sure if this could be valid because I didnt found any 
literature of such NMA in Gromacs. Could someone provide me with the 
appropriate cut-offs for the NMA in gromacs?


These are particular to the force field involved, not the software. 
Please consult the appropriate literature, and see what others have used 
for similar work.




By the way before this NMA I've done 2 energy minimization calculations
first by Steepest algorithm (emtool= 1000) and then by CG ( emtool=10)
but resulting force was still not small enought (8.92766e+02). How I 
can futher minimize my structurere?


Smaller EM steps might do something.



Finally I've forced with the diffuculty of the analysing of my data by 
the  g_anaeig

E,g I want to obtain fluctuations of some atoms from my eigenvectors
g_anaeig -s fornma22.tpr -v eigenvec.trr -eig eigenval2.xvg -rmsf 
-first -1

1 0

I've obtained a .xvg file fith the fluctuations along 1st mode but 
during opening that file by xgrace I've obtain some input error. Whats 
I've done wrong ?


We can't tell from this information.

Mark




Thanks,
James


2011/10/23 James Starlight >


I want to come back to the question of the NMA in the Gromacs :)

I've found in manual possible algorithms of this analysis-  I must
calculate Hessian matrix via Md-run and then calculate modes with
g_nmens program


1- I've performed CG minimization of my initianl structure

2- I've loadet to the gromp .tpr file of my minimized structure

3-  I've used mdrun and obtain error
Fatal error:
Constraints present with Normal Mode Analysis, this combination is
not supported

So I suppose that the problem with my .mdp file wich consist of
the parametres for the NMA of Lyzosyme in water :)

integrator= nm; Normal Mode Analysis

; Parameters describing how to find the neighbors of each atom and
how to calculate the interactions
nstlist= 1; Frequency to update the neighbor list
and long range forces
ns_type= grid; Method to determine neighbor list
(simple, grid)
rlist= 1.0; Cut-off for making neighbor list
(short range forces)
coulombtype= PME; Treatment of long range
electrostatic interactions
rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)


How I should edit this configure file for my NMA?
If I edit the above parametries for rvdw etc in accardance to the

http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nm
I've obtained error that

ERROR 1 [file nma.mdp]:
  With coulombtype = PME, rcoulomb must be equal to rlist
  If you want optimal energy conservation or exact integration use
PME-Switch


ERROR 2 [file nma.mdp]:
  With vdwtype = Cut-off, rvdw must be >= rlist

What are the most suitable coulombtype for the NMA and combination
of the other options?


James







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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 24/10/2011 3:12 AM, James Starlight wrote:

I want to come back to the question of the NMA in the Gromacs :)

I've found in manual possible algorithms of this analysis-  I must 
calculate Hessian matrix via Md-run and then calculate modes with 
g_nmens program



1- I've performed CG minimization of my initianl structure

2- I've loadet to the gromp .tpr file of my minimized structure

3-  I've used mdrun and obtain error
Fatal error:
Constraints present with Normal Mode Analysis, this combination is not 
supported


So I suppose that the problem with my .mdp file wich consist of the 
parametres for the NMA of Lyzosyme in water :)


integrator= nm; Normal Mode Analysis

; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions
nstlist= 1; Frequency to update the neighbor list and 
long range forces
ns_type= grid; Method to determine neighbor list 
(simple, grid)
rlist= 1.0; Cut-off for making neighbor list (short 
range forces)
coulombtype= PME; Treatment of long range electrostatic 
interactions

rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)


How I should edit this configure file for my NMA?
If I edit the above parametries for rvdw etc in accardance to the 
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nm 
I've obtained error that


ERROR 1 [file nma.mdp]:
  With coulombtype = PME, rcoulomb must be equal to rlist
  If you want optimal energy conservation or exact integration use 
PME-Switch



ERROR 2 [file nma.mdp]:
  With vdwtype = Cut-off, rvdw must be >= rlist

What are the most suitable coulombtype for the NMA and combination of 
the other options?


That .mdp file did not produce that output.

Mark
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

As the consequence I've done my NMA calculations without of any constraints
:)

integrator= nm; Normal Mode Analysis
constraints =  none


but I'm not sure if this could be valid because I didnt found any literature
of such NMA in Gromacs. Could someone provide me with the appropriate
cut-offs for the NMA in gromacs?

By the way before this NMA I've done 2 energy minimization calculations
first by Steepest algorithm (emtool= 1000) and then by CG ( emtool=10)
but resulting force was still not small enought (8.92766e+02). How I can
futher minimize my structurere?

Finally I've forced with the diffuculty of the analysing of my data by the
g_anaeig
E,g I want to obtain fluctuations of some atoms from my eigenvectors
g_anaeig -s fornma22.tpr -v eigenvec.trr -eig eigenval2.xvg -rmsf -first -1
1 0

I've obtained a .xvg file fith the fluctuations along 1st mode but during
opening that file by xgrace I've obtain some input error. Whats I've done
wrong ?


Thanks,
James


2011/10/23 James Starlight 

> I want to come back to the question of the NMA in the Gromacs :)
>
> I've found in manual possible algorithms of this analysis-  I must
> calculate Hessian matrix via Md-run and then calculate modes with g_nmens
> program
>
>
> 1- I've performed CG minimization of my initianl structure
>
> 2- I've loadet to the gromp .tpr file of my minimized structure
>
> 3-  I've used mdrun and obtain error
> Fatal error:
> Constraints present with Normal Mode Analysis, this combination is not
> supported
>
> So I suppose that the problem with my .mdp file wich consist of the
> parametres for the NMA of Lyzosyme in water :)
>
> integrator= nm; Normal Mode Analysis
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist= 1; Frequency to update the neighbor list and long
> range forces
> ns_type= grid; Method to determine neighbor list (simple,
> grid)
> rlist= 1.0; Cut-off for making neighbor list (short range
> forces)
> coulombtype= PME; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.0; Short-range electrostatic cut-off
> rvdw= 1.0; Short-range Van der Waals cut-off
> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>
>
> How I should edit this configure file for my NMA?
> If I edit the above parametries for rvdw etc in accardance to the
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nmI've
>  obtained error that
>
> ERROR 1 [file nma.mdp]:
>   With coulombtype = PME, rcoulomb must be equal to rlist
>   If you want optimal energy conservation or exact integration use
> PME-Switch
>
>
> ERROR 2 [file nma.mdp]:
>   With vdwtype = Cut-off, rvdw must be >= rlist
>
> What are the most suitable coulombtype for the NMA and combination of the
> other options?
>
>
> James
>
>
>
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

I want to come back to the question of the NMA in the Gromacs :)

I've found in manual possible algorithms of this analysis-  I must calculate
Hessian matrix via Md-run and then calculate modes with g_nmens program


1- I've performed CG minimization of my initianl structure

2- I've loadet to the gromp .tpr file of my minimized structure

3-  I've used mdrun and obtain error
Fatal error:
Constraints present with Normal Mode Analysis, this combination is not
supported

So I suppose that the problem with my .mdp file wich consist of the
parametres for the NMA of Lyzosyme in water :)

integrator= nm; Normal Mode Analysis

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long
range forces
ns_type= grid; Method to determine neighbor list (simple,
grid)
rlist= 1.0; Cut-off for making neighbor list (short range
forces)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)


How I should edit this configure file for my NMA?
If I edit the above parametries for rvdw etc in accardance to the
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nmI've
obtained error that

ERROR 1 [file nma.mdp]:
  With coulombtype = PME, rcoulomb must be equal to rlist
  If you want optimal energy conservation or exact integration use
PME-Switch


ERROR 2 [file nma.mdp]:
  With vdwtype = Cut-off, rvdw must be >= rlist

What are the most suitable coulombtype for the NMA and combination of the
other options?


James
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Re: [gmx-users] Normal Mode Analysis

[Mark Abraham]

On 16/10/2011 4:31 AM, James Starlight wrote:

Thanks
It's  works fine but I'venot find significant increasing in the 
simulation speed :)


If you've configured with threads, then executing mdrun will spawn as 
many threads as you have physical cores. This will speed up the 
calculation so long as it runs for more than a few seconds.


but I'd also to test MPI. Could you tell me what exactly ( MPI or 
threading) might provide better productivity in case of big 
heterogenious system ( e.g protein in membrane )?


It depends. MPI is required if your processors are not on the same piece 
of silicon, and is almost as good as threading if they are. Threading 
works if they are.


Mark




James

2011/10/15 lina mailto:lina.lastn...@gmail.com>>

On Sat, Oct 15, 2011 at 2:58 AM, James Starlight
mailto:jmsstarli...@gmail.com>> wrote:
> Dear Gromacs users!
>
> I have couple of questions about some Gromacs features.
>
>
> 1- I'm looking for tutorial where I could find clear example of 
force fied

> based Normal Mode Analysis via Gromacs
>
> E.g on first step I would like to prepare structure of my protein in
> pereodic boundary conditions and conduct energy minimization (
I've already
> can do it). Next I'd like to conduct full-atomic Normal Mode
analysis and
> obtain motion trajectories along some lowest frequency modes for
futher
> visualization in VMD. Finally I'd like to obtain information about
> frequencies ( eigenvalues) of each mode as well as frequencies
of each
> residue fluctuations along different modes.
>
>
> 2- Also I'm looking for possible ways to enhanse Gromacs
efficiency eg via
> ussage of multi cores of my CPU. I've found possible sillution
via MPI
> function but this way dowsnt work in my case. How I can activate
> hyperthreading function as well as other possible ways ?

If you installed from src, during configure
--enable-threads

if you installed via some package management tools, I guess they would
install this way by default.

try:

mdrun -t

>
>
> Thank you for your help
>
> James
>
> --
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Re: [gmx-users] Normal Mode Analysis

[James Starlight]

Thanks
It's  works fine but I'venot find significant increasing in the simulation
speed :)
but I'd also to test MPI. Could you tell me what exactly ( MPI or threading)
might provide better productivity in case of big heterogenious system ( e.g
protein in membrane )?


James

2011/10/15 lina 

> On Sat, Oct 15, 2011 at 2:58 AM, James Starlight 
> wrote:
> > Dear Gromacs users!
> >
> > I have couple of questions about some Gromacs features.
> >
> >
> > 1- I'm looking for tutorial where I could find clear example of  force
> fied
> > based Normal Mode Analysis via Gromacs
> >
> > E.g on first step I would like to prepare structure of my protein in
> > pereodic boundary conditions and conduct energy minimization ( I've
> already
> > can do it). Next I'd like to conduct full-atomic Normal Mode analysis and
> > obtain motion trajectories along some lowest frequency modes for futher
> > visualization in VMD. Finally I'd like to obtain information about
> > frequencies ( eigenvalues) of each mode as well as frequencies of each
> > residue fluctuations along different modes.
> >
> >
> > 2- Also I'm looking for possible ways to enhanse Gromacs efficiency eg
> via
> > ussage of multi cores of my CPU. I've found possible sillution via MPI
> > function but this way dowsnt work in my case. How I can activate
> > hyperthreading function as well as other possible ways ?
>
> If you installed from src, during configure
> --enable-threads
>
> if you installed via some package management tools, I guess they would
> install this way by default.
>
> try:
>
> mdrun -t
>
> >
> >
> > Thank you for your help
> >
> > James
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> >
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Re: [gmx-users] Normal Mode Analysis

[lina]

On Sat, Oct 15, 2011 at 2:58 AM, James Starlight  wrote:
> Dear Gromacs users!
>
> I have couple of questions about some Gromacs features.
>
>
> 1- I'm looking for tutorial where I could find clear example of  force fied
> based Normal Mode Analysis via Gromacs
>
> E.g on first step I would like to prepare structure of my protein in
> pereodic boundary conditions and conduct energy minimization ( I've already
> can do it). Next I'd like to conduct full-atomic Normal Mode analysis and
> obtain motion trajectories along some lowest frequency modes for futher
> visualization in VMD. Finally I'd like to obtain information about
> frequencies ( eigenvalues) of each mode as well as frequencies of each
> residue fluctuations along different modes.
>
>
> 2- Also I'm looking for possible ways to enhanse Gromacs efficiency eg via
> ussage of multi cores of my CPU. I've found possible sillution via MPI
> function but this way dowsnt work in my case. How I can activate
> hyperthreading function as well as other possible ways ?

If you installed from src, during configure
--enable-threads

if you installed via some package management tools, I guess they would
install this way by default.

try:

mdrun -t

>
>
> Thank you for your help
>
> James
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Normal Mode Analysis

[James Starlight]

Dear Gromacs users!

I have couple of questions about some Gromacs features.


1- I'm looking for tutorial where I could find clear example of  force fied
based Normal Mode Analysis via Gromacs

E.g on first step I would like to prepare structure of my protein in
pereodic boundary conditions and conduct energy minimization ( I've already
can do it). Next I'd like to conduct full-atomic Normal Mode analysis and
obtain motion trajectories along some lowest frequency modes for futher
visualization in VMD. Finally I'd like to obtain information about
frequencies ( eigenvalues) of each mode as well as frequencies of each
residue fluctuations along different modes.


2- Also I'm looking for possible ways to enhanse Gromacs efficiency eg via
ussage of multi cores of my CPU. I've found possible sillution via MPI
function but this way dowsnt work in my case. How I can activate
hyperthreading function as well as other possible ways ?


Thank you for your help

James
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Re: [gmx-users] Normal Mode Analysis

[Ran Friedman]

Hi,

NMA is not MD - for one thing you don't run an NMA simulation for a
certain time. I suggest you read about NMA and make sure you understand
what the method does and what it can achieve before continuing. There is
some data on the manual, a lot of data on the web and even more in
books. When you have a good idea on what is NMA and why you're
interested in running it, you can try to run things and come back to the
list with more specific questions if such arise. In parallel, it may be
a good idea to read some papers where NMA was applied. I have in mind
papers of Lindahl and Levitt from the recent years, but you should be
able to come with an elaborate list.

Good luck,
Ran

Anirban Ghosh wrote:
>
> Hi ALL,
>
> This may sound like a very basic question, but I am still pondering
> over it. I have simulated a membrane protein system for 30 ns after
> Steepest Descent minimization and now I want to perform NMA. From the
> help pages what I understand is that I need a very well minimized
> system (using l-bfgs) and then generate a Hessian matrix. My question
> is that after my 30 ns run, should I again go for another run of
> minimization with l-bfgs and the should I run MD using "nm" as the
> integrator? For how long should I run this MD with "nm" integrator? Is
> a 1 ns run enough? Or am I required to run it for 30 ns (for which I
> have run the normal MD)?
> Any suggestion is welcome. Thanks a lot in advance.
>
> Regards,
>
> Anirban

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[gmx-users] Normal Mode Analysis

[Anirban Ghosh]

Hi ALL,

This may sound like a very basic question, but I am still pondering over it.
I have simulated a membrane protein system for 30 ns after Steepest Descent
minimization and now I want to perform NMA. From the help pages what I
understand is that I need a very well minimized system (using l-bfgs) and
then generate a Hessian matrix. My question is that after my 30 ns run,
should I again go for another run of minimization with l-bfgs and the should
I run MD using "nm" as the integrator? For how long should I run this MD
with "nm" integrator? Is a 1 ns run enough? Or am I required to run it for
30 ns (for which I have run the normal MD)?
Any suggestion is welcome. Thanks a lot in advance.

Regards,

Anirban
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[gmx-users] Normal Mode Analysis

[Anirban Ghosh]

Hi ALL,

This may sound like a very basic question, but I am still pondering over it.
I have simulated a membrane protein system for 30 ns after Steepest Descent
minimization and now I want to perform NMA. From the help pages what I
understand is that I need a very well minimized system (using l-bfgs) and
then generate a Hessian matrix. My question is that after my 30 ns run,
should I again go for another run of minimization with l-bfgs and the should
I run MD using "nm" as the integrator? For how long should I run this MD
with "nm" integrator? Is a 1 ns run enough? Or am I required to run it for
30 ns (for which I have run the normal MD)?
Any suggestion is welcome. Thanks a lot in advance.

Regards,

Anirban
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Re: [gmx-users] Normal Mode analysis

[KS Rotondi]

I'm joining the tautology society as well... : ) The by-line is, "if  
we get 100,000 members, we'll have 100,000 members..."

On Feb 20, 2010, at 4:28 PM, Tsjerk Wassenaar wrote:


Aside from that, search the literature; published papers should have
reproducible methodology :)


And.., methodology in published papers has proven to be publishable.

:)

Tsjerk

--
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Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Normal Mode analysis

[Tsjerk Wassenaar]

> Aside from that, search the literature; published papers should have
> reproducible methodology :)

And.., methodology in published papers has proven to be publishable.

:)

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] Normal Mode analysis

[Justin A. Lemkul]

Ajit Datta wrote:

Hello everyone,
  I am trying to do normal mode analysis for a protein using Gromacs. 
Can anyone point me out towards a sample mdp file that I could edit for this 
purpose?


There are some general pointers here:

http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

Aside from that, search the literature; published papers should have 
reproducible methodology :)


-Justin


Thanks

Ajit B.


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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Normal Mode analysis

[Ajit Datta]

Hello everyone,
  I am trying to do normal mode analysis for a protein using Gromacs. 
Can anyone point me out towards a sample mdp file that I could edit for this 
purpose?
Thanks

Ajit B.
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[gmx-users] normal mode analysis

[abhijit kayal]

Hi Gromacs User's,
In the normal mode analysis if I get the first 6 eigenfrequency zero
then I can think that the the protein is properly energy  minimized.

   Thank you

  Abhijit
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Re: [gmx-users] Normal mode analysis of pure water

[Justin A. Lemkul]

simon sangma wrote:

Hi  Justin,
Are you suggesting that after thorough energy 
minimization, seperate .mdp file is to be used for NMA? In that case how 
would that output file (energy minimised file) be taken as an input file 
for the grompp and mdrun command (for NMA)? What extension would the 
file have (.what) ?




Yes, they are done in separate steps.  I think you need to do some tutorial 
material on the workflow of a GROMACS procedure.  Run energy minimization (in 
double precision), and the output of EM is your input for NMA (the minimized 
structure).


-Justin





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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Normal mode analysis of pure water

[simon sangma]

Hi Berk,
 I want to determine the vibrational frequencies of water (close
to the experimentally observed values for the three modes). And then extend
the analogy for more complex systems.
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[gmx-users] Normal mode analysis of pure water

[simon sangma]

Hi  Justin,
Are you suggesting that after thorough energy minimization,
seperate .mdp file is to be used for NMA? In that case how would that output
file (energy minimised file) be taken as an input file for the grompp and
mdrun command (for NMA)? What extension would the file have (.what) ?
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RE: [gmx-users] Normal mode analysis of pure water

[Berk Hess]

You could get better help if you tell us what information you want to get out 
of this analysis.

NMA gives you a harmonic description of the potential energy around a minimum 
of the system.
For water the minimum is ice, so you would get the modes of a certain ice state.

Berk

Date: Tue, 20 Oct 2009 19:20:19 +0530
From: simoniitc...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Normal mode analysis of pure water

Hi Berk,
 You mentioned that standard NMA techniques will not work for the 
liquid water  system. Could you suggest the alternatives then?
  
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[gmx-users] Normal mode analysis of pure water

[simon sangma]

Hi Berk,
 You mentioned that standard NMA techniques will not work for
the liquid water  system. Could you suggest the alternatives then?
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RE: [gmx-users] Normal mode analysis of pure water

[Berk Hess]

This is wasting a large amount of CPU time.
Water is solid (ice) at 0 K.
A plain normal mode analysis would give you the normal modes of ice.
You can do a normal mode analysis of liquid water without minimization,
but the standard NMA techniques will not work.

Berk

Date: Tue, 20 Oct 2009 18:33:43 +0530
From: simoniitc...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Normal mode analysis of pure water

Hi,
I encountered the following remarks during normal mode analysis of pure 
water. Can someone please suggest a solution.
 mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx 
nm.mtx
Getting Loaded...

Reading file water.tpr, VERSION 4.0.4 (double precision)
Loaded with Money

Non-cutoff electrostatics used, forcing full Hessian format.
Allocating Hessian memory...

starting normal mode calculation 'Pure Water'

648 steps.

Maximum force: 2.74758e+03
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.

Finished step 648 out of 648

Writing Hessian...

gcq#258: "In the End Science Comes Down to Praying" (P. v.d. Berg)

g_nmeig_d -f nm.mtx -s water.tpr -of eigenfreq.xvg -ol eigenval.xvg -v 
eigenvec.trr


Reading file water.tpr, VERSION 4.0.4 (double precision)
Reading file water.tpr, VERSION 4.0.4 (double precision)
Reading double precision matrix generated by Gromacs VERSION 4.0.4
Full matrix storage format, nrow=1944, ncols=1944


Diagonalizing to find vectors 1 through 50...

One of the lowest 6 eigenvalues has a non-zero value.
This could mean that the reference structure was not
properly energy minimized.
Writing eigenvalues...

Writing eigenfrequencies - negative eigenvalues will be set to zero.

Writing average structure & eigenvectors 1--50 to eigenvec.trr

gcq#132: "Shit Happens" (Pulp Fiction)


The eigenfreq is 0 which is the problem


The .mdp file used was;
;   User spoel (236)
;   Wed Nov  3 17:12:44 1993
;   Input file
;
cpp =
define  =  -DFLEXIBLE
constraints =  none
integrator  =  nm

nsteps  =  1
;
;   Energy minimizing stuff
;
emtol   =  0.01
emstep  =  0.01
coulombtype =  PME
nstcomm =  1
ns_type =  grid

rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no




  
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Re: [gmx-users] Normal mode analysis of pure water

[Justin A. Lemkul]

simon sangma wrote:

Hi  Justin,
I tried  altering  the  .mdp file  (integrator  =  
steep  instead  of nm) for energy  minimization. But in that case the 
mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the 
command twice.




Energy minimization is not the same thing as Normal Mode Analysis.  You have to 
energy minimize your system (thoroughly!) first, then run NMA.


-Justin





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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Normal mode analysis of pure water

[simon sangma]

Hi  Justin,
I tried  altering  the  .mdp file  (integrator  =  steep
instead  of nm) for energy  minimization. But in that case the mdrun did not
generate the Hessian matrix (nm.mtx) inspite of using the command twice.
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Re: [gmx-users] Normal mode analysis of pure water

[Justin A. Lemkul]

simon sangma wrote:

Hi,
I encountered the following remarks during normal mode analysis of 
pure water. Can someone please suggest a solution.


You've been told twice already what the likely solution is:




Maximum force: 2.74758e+03
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.





One of the lowest 6 eigenvalues has a non-zero value.
This could mean that the reference structure was not
properly energy minimized.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Normal mode analysis of pure water

[simon sangma]

Hi,
I encountered the following remarks during normal mode analysis of pure
water. Can someone please suggest a solution.
 mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log
-mtx nm.mtx
Getting Loaded...
Reading file water.tpr, VERSION 4.0.4 (double precision)
Loaded with Money

Non-cutoff electrostatics used, forcing full Hessian format.
Allocating Hessian memory...

starting normal mode calculation 'Pure Water'
648 steps.

Maximum force: 2.74758e+03
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.
Finished step 648 out of 648

Writing Hessian...

gcq#258: "In the End Science Comes Down to Praying" (P. v.d. Berg)

g_nmeig_d -f nm.mtx -s water.tpr -of eigenfreq.xvg -ol eigenval.xvg -v
eigenvec.trr

Reading file water.tpr, VERSION 4.0.4 (double precision)
Reading file water.tpr, VERSION 4.0.4 (double precision)
Reading double precision matrix generated by Gromacs VERSION 4.0.4
Full matrix storage format, nrow=1944, ncols=1944

Diagonalizing to find vectors 1 through 50...

One of the lowest 6 eigenvalues has a non-zero value.
This could mean that the reference structure was not
properly energy minimized.
Writing eigenvalues...
Writing eigenfrequencies - negative eigenvalues will be set to zero.

Writing average structure & eigenvectors 1--50 to eigenvec.trr

gcq#132: "Shit Happens" (Pulp Fiction)


The eigenfreq is 0 which is the problem

The .mdp file used was;
;   User spoel (236)
;   Wed Nov  3 17:12:44 1993
;   Input file
;
cpp =
define  =  -DFLEXIBLE
constraints =  none
integrator  =  nm
nsteps  =  1
;
;   Energy minimizing stuff
;
emtol   =  0.01
emstep  =  0.01
coulombtype =  PME
nstcomm =  1
ns_type =  grid
rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
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Re: [gmx-users] Normal mode analysis

[Justin A. Lemkul]

abhijit kayal wrote:

Hi,
 If I going to perform normal mode analysis of a protien 
molecule what are the changes have to be done in .mdp files
 


That's what the manual is for, as well as pertinent literature and textbooks 
describing the protocols.


-Justin


Abhijit Kayal
 IIT Delhi




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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Normal mode analysis

[abhijit kayal]

Hi,
 If I going to perform normal mode analysis of a protien molecule
what are the changes have to be done in .mdp files
   Abhijit
Kayal
 IIT Delhi
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Re: [gmx-users] Normal mode analysis

[Mark Abraham]

simon sangma wrote:

Hi!
 I am a user of gromacs. Could someone provide me with a method (or set
of commands) for normal mode analysis of small molecules (water, n-butane,
etc). Also could you please provide a command for generating Hessian Matrix
after the energy minimization.


You should start by reading the section of the manual that deals with 
these techniques.


You're far more likely to get helpful responses if you demonstrate that 
you're prepared to work towards your goals (i.e. read documentation, try 
commands out) and have specific, focussed questions.


Mark
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[gmx-users] Normal mode analysis

[simon sangma]

Hi!
 I am a user of gromacs. Could someone provide me with a method (or set
of commands) for normal mode analysis of small molecules (water, n-butane,
etc). Also could you please provide a command for generating Hessian Matrix
after the energy minimization.
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Re: [gmx-users] Normal Mode Analysis

[Franzi Hoffgaard]

Hi,

I don't know exactly what went wrong when I tried to patch the file. There
was a > on line 18 in the fix file, actually. I checked it. With the file
you sent me, gmxdump works fine.

Thank you very much for your help.

Best regards, Franzi

---
Franziska Hoffgaard
PhD Student
Bioinformatics & Theo. Biology Group
TU Darmstadt


2009/5/26 Berk Hess 

>  Hi,
>
> But there is a '>' on line 18, at least in my mail.
> I tested the patch and it worked for me.
> Maybe something went wrong when cut and pasting the patch from the email?
> I can mail you the whole file personally tomorrow, if required.
>
> Berk
>
> --
> Date: Tue, 26 May 2009 14:47:52 +0200
> Subject: Re: [gmx-users] Normal Mode Analysis
> From: f.hoffga...@gmail.com
> To: gmx-users@gromacs.org
>
> Hi
>
> thanks for your reply. I tried patching as you described it, but I got the
> error message:
>
> patch:  `>' expected at line 18 of patch
>
> Franzi
>
> ---
> Franziska Hoffgaard
> PhD Student
> Bioinformatics & Theo. Biology Group
> TU Darmstadt
>
> 2009/5/26 Berk Hess 
>
>  Hi,
>
> I just saw that 4.0 uses a new mtx format which can also efficiently store
> sparse matrices.
> Please try if my modified gmxdump for 4.0.5 works?
> Store the data below in a file called fix and then do:
> patch gmxdump.c fix
>
> Berk
>
> 61a62,63
> > #include "sparsematrix.h"
> > #include "mtxio.h"
> 364a367,402
> > static void list_mtx(char *fn)
> > {
> >   int  nrow,ncol,i,j,k;
> >   real *full=NULL,value;
> >   gmx_sparsematrix_t * sparse=NULL;
> >
> >   gmx_mtxio_read(fn,&nrow,&ncol,&full,&sparse);
> >
> >   if (full == NULL) {
> > snew(full,nrow*ncol);
> > for(i=0;i >   full[i] = 0;
> > }
> >
> > for(i=0;inrow;i++) {
> >   for(j=0;jndata[i];j++) {
> > k = sparse->data[i][j].col;
> > value = sparse->data[i][j].value;
> > full[i*ncol+k] = value;
> > full[k*ncol+i] = value;
> >   }
> > }
> > gmx_sparsematrix_destroy(sparse);
> >   }
> >
> >   printf("%d %d\n",nrow,ncol);
> >   for(i=0; i > for(j=0; j >   printf(" %g",full[i*ncol+j]);
> > }
> > printf("\n");
> >   }
> >
> >   sfree(full);
> > }
> >
> 381a420
> > { efMTX, "-mtx", "hessian", ffOPTRD },
> 409a449,450
> >   else if (ftp2bSet(efMTX,NFILE,fnm))
> > list_mtx(ftp2fn(efMTX,NFILE,fnm));
>
>
> --
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RE: [gmx-users] Normal Mode Analysis

[Berk Hess]

Hi,

But there is a '>' on line 18, at least in my mail.
I tested the patch and it worked for me.
Maybe something went wrong when cut and pasting the patch from the email?
I can mail you the whole file personally tomorrow, if required.

Berk

Date: Tue, 26 May 2009 14:47:52 +0200
Subject: Re: [gmx-users] Normal Mode Analysis
From: f.hoffga...@gmail.com
To: gmx-users@gromacs.org

Hi

thanks for your reply. I tried patching as you described it, but I got the 
error message:

patch:  `>' expected at line 18 of patch

Franzi

---
Franziska Hoffgaard
PhD Student

Bioinformatics & Theo. Biology Group
TU Darmstadt

2009/5/26 Berk Hess 






Hi,

I just saw that 4.0 uses a new mtx format which can also efficiently store 
sparse matrices.
Please try if my modified gmxdump for 4.0.5 works?
Store the data below in a file called fix and then do:
patch gmxdump.c fix


Berk

61a62,63 
> #include "sparsematrix.h"  
> #include "mtxio.h" 
364a367,402  

> static void list_mtx(char *fn) 
> {  
>   int  nrow,ncol,i,j,k;
>   real *full=NULL,value;   

>   gmx_sparsematrix_t * sparse=NULL;
>
>   gmx_mtxio_read(fn,&nrow,&ncol,&full,&sparse);
>

>   if (full == NULL) {
> snew(full,nrow*ncol);
> for(i=0;i   full[i] = 0;
> }
>
> for(i=0;inrow;i++) {
>   for(j=0;jndata[i];j++) {

> k = sparse->data[i][j].col;
> value = sparse->data[i][j].value;
> full[i*ncol+k] = value;
> full[k*ncol+i] = value;
>   }
> }
> gmx_sparsematrix_destroy(sparse);

>   }
>
>   printf("%d %d\n",nrow,ncol);
>   for(i=0; i for(j=0; j   printf(" %g",full[i*ncol+j]);
> }
> printf("\n");

>   }
>
>   sfree(full);
> }
>
381a420
> { efMTX, "-mtx", "hessian", ffOPTRD },
409a449,450
>   else if (ftp2bSet(efMTX,NFILE,fnm))
> list_mtx(ftp2fn(efMTX,NFILE,fnm));



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Re: [gmx-users] Normal Mode Analysis

[Franzi Hoffgaard]

Hi

thanks for your reply. I tried patching as you described it, but I got the
error message:

patch:  `>' expected at line 18 of patch

Franzi

---
Franziska Hoffgaard
PhD Student
Bioinformatics & Theo. Biology Group
TU Darmstadt

2009/5/26 Berk Hess 

>  Hi,
>
> I just saw that 4.0 uses a new mtx format which can also efficiently store
> sparse matrices.
> Please try if my modified gmxdump for 4.0.5 works?
> Store the data below in a file called fix and then do:
> patch gmxdump.c fix
>
> Berk
>
> 61a62,63
> > #include "sparsematrix.h"
> > #include "mtxio.h"
> 364a367,402
> > static void list_mtx(char *fn)
> > {
> >   int  nrow,ncol,i,j,k;
> >   real *full=NULL,value;
> >   gmx_sparsematrix_t * sparse=NULL;
> >
> >   gmx_mtxio_read(fn,&nrow,&ncol,&full,&sparse);
> >
> >   if (full == NULL) {
> > snew(full,nrow*ncol);
> > for(i=0;i >   full[i] = 0;
> > }
> >
> > for(i=0;inrow;i++) {
> >   for(j=0;jndata[i];j++) {
> > k = sparse->data[i][j].col;
> > value = sparse->data[i][j].value;
> > full[i*ncol+k] = value;
> > full[k*ncol+i] = value;
> >   }
> > }
> > gmx_sparsematrix_destroy(sparse);
> >   }
> >
> >   printf("%d %d\n",nrow,ncol);
> >   for(i=0; i > for(j=0; j >   printf(" %g",full[i*ncol+j]);
> > }
> > printf("\n");
> >   }
> >
> >   sfree(full);
> > }
> >
> 381a420
> > { efMTX, "-mtx", "hessian", ffOPTRD },
> 409a449,450
> >   else if (ftp2bSet(efMTX,NFILE,fnm))
> > list_mtx(ftp2fn(efMTX,NFILE,fnm));
>
>
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RE: [gmx-users] Normal Mode Analysis

[Berk Hess]

Hi,

I just saw that 4.0 uses a new mtx format which can also efficiently store 
sparse matrices.
Please try if my modified gmxdump for 4.0.5 works?
Store the data below in a file called fix and then do:
patch gmxdump.c fix

Berk

61a62,63 
> #include "sparsematrix.h"  
> #include "mtxio.h" 
364a367,402  
> static void list_mtx(char *fn) 
> {  
>   int  nrow,ncol,i,j,k;
>   real *full=NULL,value;   
>   gmx_sparsematrix_t * sparse=NULL;
>
>   gmx_mtxio_read(fn,&nrow,&ncol,&full,&sparse);
>
>   if (full == NULL) {
> snew(full,nrow*ncol);
> for(i=0;i   full[i] = 0;
> }
>
> for(i=0;inrow;i++) {
>   for(j=0;jndata[i];j++) {
> k = sparse->data[i][j].col;
> value = sparse->data[i][j].value;
> full[i*ncol+k] = value;
> full[k*ncol+i] = value;
>   }
> }
> gmx_sparsematrix_destroy(sparse);
>   }
>
>   printf("%d %d\n",nrow,ncol);
>   for(i=0; i for(j=0; j   printf(" %g",full[i*ncol+j]);
> }
> printf("\n");
>   }
>
>   sfree(full);
> }
>
381a420
> { efMTX, "-mtx", "hessian", ffOPTRD },
409a449,450
>   else if (ftp2bSet(efMTX,NFILE,fnm))
> list_mtx(ftp2fn(efMTX,NFILE,fnm));


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Re: [gmx-users] Normal Mode Analysis

[Franzi Hoffgaard]

Hi,

as I wrote in the first message, I tried renaming it with the extension .trj
and yielded segmentation faults. I also tried it with the extension .trr and
got the error message:

trn version: VERSION 4.0.4
---
Program gmxdump_d, VERSION 4.0.4
Source code file: trnio.c, line: 69

Fatal error:
Float size 3556. Maybe different CPU?
---

Both extensions didn't work.


There is just another little question that came into my mind. As I said I
performed the NMA with gromacs 3.2.1 and 4.0.x both with the same system and
setup. I would expect that the .mtx-files have similar sizes, but using
version 4.0.x the file-size is about 300 Mb and using the version 3.2.1 it
is about 7 Gb.

Franzi



2009/5/26 Berk Hess 

>  Hi,
>
> Try renaming it with the extension .trr iso .trj.
>
> Berk
>
> --
> Date: Tue, 26 May 2009 10:53:32 +0200
> From: f.hoffga...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Normal Mode Analysis
>
>
> Hi,
>
> I'm quite a new user of gromacs. I want to do an all-atom normal mode
> analysis of a small protein in water. As a result I would like to have the
> hessian matrix in a readable format, that I can use for further
> computations.
>
> As I have read in the manuals/tutorials/mailing-lists I minimized the whole
> system (at first with the steepest descent integrator for a couple of steps
> and later on with the l-bfgs integrator to become a maximum force close to
> zero). Afterwards I created the run input file (with the nm integrator)
> using the high precision trajectory from the minimization. This and the
> following call of mdrun worked fine. As a result I became the hessian.mtx.
>
> As I said I want the matrix in ASCII format, so I followed the instructions
> and renamed the file into hessian.trj and ran "gmxdump_d -f mat2.trj" and
> got a Segmentation fault.Trying gmxcheck also led to Segmentation fault. I
> tried same procedure but using trr instead of trj as file-ending. Both, for
> gmxcheck and gmxdump I yielded the following message:
>
> trn version: VERSION 4.0.4
> ---
> Program gmxdump_d, VERSION 4.0.4
> Source code file: trnio.c, line: 69
>
> Fatal error:
> Float size 3556. Maybe different CPU?
> ---
>
> I tried "g_traj -ox" as well without any result. This led me to the
> conclusion that the file is corrupt, but I just tried diagonalizing the
> hessian matrix using "g_nmeig" anyway. Surprisingly this yielded no error
> message and I ended up with the first 50 eigenvalues and -vectors. So
> despite my first assumption the file cannot be corrupt. Or am I wrong?
>
> The architecture/s I worked on are:
> 1. Suse Linux 10.3, 64 bit, Intel Processor, quad-core (gromacs 4.0.3)
> 2. Mac OS X 10.5 (Leopard), Intel Proc. 2 x quad-core (gromacs 4.0.4,
> gromacs 4.0.5)
>
> The results were on both architectures the same. But ...
>
> I read in a former email of this mailing list of a similar problem and that
> the problem did not occur in the gromacs version 3.2.1. So I uninstalled
> gromacs 4.0 and installed gromacs 3.2.1 and  performed the last stage of
> minimization and the computation of the hessian matrix. This binary file
> yielded no error using gmxdump and gmxcheck. (Input files for the l-bfgs and
> nm step were not changed.)
>
> So, my question is, is this a bug of the newer gromacs version/s or did I
> something wrong. As I would like to stick to a newer version of gromacs, I
> am wondering, what else (than downgrading) can I do to get the hessian
> matrix in a human readable format out of the normal mode analysis.
>
> Best regards, Franziska
>
> ---
> Franziska Hoffgaard
> PhD Student
> Bioinformatics & Theo. Biology Group
> TU Darmstadt
>
>
>
> --
> Express yourself instantly with MSN Messenger! MSN 
> Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
>
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RE: [gmx-users] Normal Mode Analysis

[Berk Hess]

Hi,

Try renaming it with the extension .trr iso .trj.

Berk

Date: Tue, 26 May 2009 10:53:32 +0200
From: f.hoffga...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Normal Mode Analysis

Hi,

I'm quite a new user of gromacs. I want to do an all-atom normal mode analysis 
of a small protein in water. As a result I would like to have the hessian 
matrix in a readable format, that I can use for further computations.



As I have read in the manuals/tutorials/mailing-lists I minimized the whole 
system (at first with the steepest descent integrator for a couple of steps and 
later on with the l-bfgs integrator to become a maximum force close to zero). 
Afterwards I created the run input file (with the nm integrator) using the high 
precision trajectory from the minimization. This and the following call of 
mdrun worked fine. As a result I became the hessian.mtx.



As I said I want the matrix in ASCII format, so I followed the instructions and 
renamed the file into hessian.trj and ran "gmxdump_d -f mat2.trj" and got a 
Segmentation fault.Trying gmxcheck also led to Segmentation fault. I tried same 
procedure but using trr instead of trj as file-ending. Both, for gmxcheck and 
gmxdump I yielded the following message:



trn version: VERSION 4.0.4
---
Program gmxdump_d, VERSION 4.0.4
Source code file: trnio.c, line: 69

Fatal error:
Float size 3556. Maybe different CPU?


---

I tried "g_traj -ox" as well without any result. This led me to the conclusion 
that the file is corrupt, but I just tried diagonalizing the hessian matrix 
using "g_nmeig" anyway. Surprisingly this yielded no error message and I ended 
up with the first 50 eigenvalues and -vectors. So despite my first assumption 
the file cannot be corrupt. Or am I wrong?



The architecture/s I worked on are:
1. Suse Linux 10.3, 64 bit, Intel Processor, quad-core (gromacs 4.0.3)
2. Mac OS X 10.5 (Leopard), Intel Proc. 2 x quad-core (gromacs 4.0.4, gromacs 
4.0.5)

The results were on both architectures the same. But ...



I read in a former email of this mailing list of a similar problem and that the 
problem did not occur in the gromacs version 3.2.1. So I uninstalled gromacs 
4.0 and installed gromacs 3.2.1 and  performed the last stage of minimization 
and the computation of the hessian matrix. This binary file yielded no error 
using gmxdump and gmxcheck. (Input files for the l-bfgs and nm step were not 
changed.)



So, my question is, is this a bug of the newer gromacs version/s or did I 
something wrong. As I would like to stick to a newer version of gromacs, I am 
wondering, what else (than downgrading) can I do to get the hessian matrix in a 
human readable format out of the normal mode analysis.



Best regards, Franziska

---
Franziska Hoffgaard
PhD Student
Bioinformatics & Theo. Biology Group
TU Darmstadt



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[gmx-users] Normal Mode Analysis

[Franzi Hoffgaard]

Hi,

I'm quite a new user of gromacs. I want to do an all-atom normal mode
analysis of a small protein in water. As a result I would like to have the
hessian matrix in a readable format, that I can use for further
computations.

As I have read in the manuals/tutorials/mailing-lists I minimized the whole
system (at first with the steepest descent integrator for a couple of steps
and later on with the l-bfgs integrator to become a maximum force close to
zero). Afterwards I created the run input file (with the nm integrator)
using the high precision trajectory from the minimization. This and the
following call of mdrun worked fine. As a result I became the hessian.mtx.

As I said I want the matrix in ASCII format, so I followed the instructions
and renamed the file into hessian.trj and ran "gmxdump_d -f mat2.trj" and
got a Segmentation fault.Trying gmxcheck also led to Segmentation fault. I
tried same procedure but using trr instead of trj as file-ending. Both, for
gmxcheck and gmxdump I yielded the following message:

trn version: VERSION 4.0.4
---
Program gmxdump_d, VERSION 4.0.4
Source code file: trnio.c, line: 69

Fatal error:
Float size 3556. Maybe different CPU?
---

I tried "g_traj -ox" as well without any result. This led me to the
conclusion that the file is corrupt, but I just tried diagonalizing the
hessian matrix using "g_nmeig" anyway. Surprisingly this yielded no error
message and I ended up with the first 50 eigenvalues and -vectors. So
despite my first assumption the file cannot be corrupt. Or am I wrong?

The architecture/s I worked on are:
1. Suse Linux 10.3, 64 bit, Intel Processor, quad-core (gromacs 4.0.3)
2. Mac OS X 10.5 (Leopard), Intel Proc. 2 x quad-core (gromacs 4.0.4,
gromacs 4.0.5)

The results were on both architectures the same. But ...

I read in a former email of this mailing list of a similar problem and that
the problem did not occur in the gromacs version 3.2.1. So I uninstalled
gromacs 4.0 and installed gromacs 3.2.1 and  performed the last stage of
minimization and the computation of the hessian matrix. This binary file
yielded no error using gmxdump and gmxcheck. (Input files for the l-bfgs and
nm step were not changed.)

So, my question is, is this a bug of the newer gromacs version/s or did I
something wrong. As I would like to stick to a newer version of gromacs, I
am wondering, what else (than downgrading) can I do to get the hessian
matrix in a human readable format out of the normal mode analysis.

Best regards, Franziska

---
Franziska Hoffgaard
PhD Student
Bioinformatics & Theo. Biology Group
TU Darmstadt
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[gmx-users] Normal mode analysis

[Polavarapu, Abhigna]

Hi All,
 I am doing normal mode analysis. After getting the eigen frequencies, 
is there a way we can visualize the vibrational modes in gromacs. And even how 
to know which frequency corresponds to which mode of vibration. I saw that IED 
is used to visualize normal modes by integrating it with VMD. But I installed 
VMD on my windows machine. So I dont think there is a way to install IED on 
windows. Please let me if there are any softwares which can visualize normal 
modes if so, how to get them?

Thank you
abhigna___
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

You can also try:
gmxdump -f em.trr | & grep precision

Inon Sharony wrote:
> The *.gro file always has 3 significant digits, but the *.tpr file
> sometimes has the coordinates with 5 significant digits and sometimes
> the last two of those are zero.
>
>
> Quoting "Ran Friedman" <[EMAIL PROTECTED]>:
>
>>
>>> How do I get a *.gro file in double-precision, then? The
>>> configurations given by the PRODRG server are in 0.000 format, and
>>> still I've at least once managed to get double-precision
> calculations
>>> out of them (right now I'm working on a file for a Pentane
> molecule,
>>> originally downloaded from PRODRG, but everything's in
>>> double-precision). I have to be doing something wrong, if I get
>>> single-precision some of the time and double-precision other
> times...
>> How many significant digits do you have in the .gro file produced
> after
>> energy minimisation?
>>
>>
>> ___
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>
> --Inon   Sharony
> ×™× ×•×Ÿ ×©×¨×•× ×™
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
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> this e-mail.
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

The *.gro file always has 3 significant digits, but the *.tpr file  
sometimes has the coordinates with 5 significant digits and sometimes  
the last two of those are zero.



Quoting "Ran Friedman" <[EMAIL PROTECTED]>:




How do I get a *.gro file in double-precision, then? The
configurations given by the PRODRG server are in 0.000 format, and
still I've at least once managed to get double-precision

calculations

out of them (right now I'm working on a file for a Pentane

molecule,

originally downloaded from PRODRG, but everything's in
double-precision). I have to be doing something wrong, if I get
single-precision some of the time and double-precision other

times...

How many significant digits do you have in the .gro file produced

after

energy minimisation?


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--
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ינון שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
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this e-mail.

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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

> How do I get a *.gro file in double-precision, then? The
> configurations given by the PRODRG server are in 0.000 format, and
> still I've at least once managed to get double-precision calculations
> out of them (right now I'm working on a file for a Pentane molecule,
> originally downloaded from PRODRG, but everything's in
> double-precision). I have to be doing something wrong, if I get
> single-precision some of the time and double-precision other times...
How many significant digits do you have in the .gro file produced after
energy minimisation?


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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

Quoting "Ran Friedman" <[EMAIL PROTECTED]>:


Inon Sharony wrote:

Dear Ran,

I'm still unsure of why I sometimes can get double-precision

output

and sometimes not. I can't find what I'm doing differently in each
case, however I now know what to look for in order to be sure that

I'm

getting what I need. Obviously, the need for double-precision

stems

only from the need to minimize the structure well before

calculating

the Hessian. When I get a maximal force of more than 1E-6 I will

get

some negative eigenvalues (which the program sets as zero) and

some

other eigenvalues which are nearly zero. In all, there are six

such

eigenmodes which I disregard as rigid-body degrees of freedom (3
translational and 3 rotational). The next modes have larger

positive

eigenvalues.

If the info in the .gro file is in single precision, the values in

the

.tpr will be with 3 significant digits and then zeros. Sorry if I

wasn't

clear about this.


How do I get a *.gro file in double-precision, then? The  
configurations given by the PRODRG server are in 0.000 format, and  
still I've at least once managed to get double-precision calculations  
out of them (right now I'm working on a file for a Pentane molecule,  
originally downloaded from PRODRG, but everything's in  
double-precision). I have to be doing something wrong, if I get  
single-precision some of the time and double-precision other times...




As for the fix in eigio.c: I made lines 110-112 into COMMENTS

(they

were not comments in the original file in the source). I

recompiled

the entire program (didn't know at the time that I can "make" only

one

function). Now the g_anaeig_d works fine (as best as I can tell).

Oops. I had the lines already commented, probably because I

corrected

this on my machine some months ago.
Ran.
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

Inon Sharony wrote:
> Dear Ran,
>
> I'm still unsure of why I sometimes can get double-precision output
> and sometimes not. I can't find what I'm doing differently in each
> case, however I now know what to look for in order to be sure that I'm
> getting what I need. Obviously, the need for double-precision stems
> only from the need to minimize the structure well before calculating
> the Hessian. When I get a maximal force of more than 1E-6 I will get
> some negative eigenvalues (which the program sets as zero) and some
> other eigenvalues which are nearly zero. In all, there are six such
> eigenmodes which I disregard as rigid-body degrees of freedom (3
> translational and 3 rotational). The next modes have larger positive
> eigenvalues.
If the info in the .gro file is in single precision, the values in the
.tpr will be with 3 significant digits and then zeros. Sorry if I wasn't
clear about this.
> As for the fix in eigio.c: I made lines 110-112 into COMMENTS (they
> were not comments in the original file in the source). I recompiled
> the entire program (didn't know at the time that I can "make" only one
> function). Now the g_anaeig_d works fine (as best as I can tell).
Oops. I had the lines already commented, probably because I corrected
this on my machine some months ago.
Ran.
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

Dear Ran,

I'm still unsure of why I sometimes can get double-precision output  
and sometimes not. I can't find what I'm doing differently in each  
case, however I now know what to look for in order to be sure that I'm  
getting what I need. Obviously, the need for double-precision stems  
only from the need to minimize the structure well before calculating  
the Hessian. When I get a maximal force of more than 1E-6 I will get  
some negative eigenvalues (which the program sets as zero) and some  
other eigenvalues which are nearly zero. In all, there are six such  
eigenmodes which I disregard as rigid-body degrees of freedom (3  
translational and 3 rotational). The next modes have larger positive  
eigenvalues.
As for the fix in eigio.c: I made lines 110-112 into COMMENTS (they  
were not comments in the original file in the source). I recompiled  
the entire program (didn't know at the time that I can "make" only one  
function). Now the g_anaeig_d works fine (as best as I can tell).

Thank you so much for all of your help!


Inon.

Quoting "Ran Friedman" <[EMAIL PROTECTED]>:


Inon Sharony wrote:

This is exactly the point - I get only three significant digits.
Although I performed the entire procedure in double-precision. The
convergence to 5E-4 DID occur in single-precision, I just thought

it

wasn't good enough (the program recommends 1E-5 and when
double-precision works for me I got 1E-6 with the files you sent

me).

What did you have in the input?
In any case if you get 6 zero frequencies and the rest are positive
you're probably fine.

I also wouldn't mind a clearer explanation of how you fixed

bugzilla

168 (see my request at


http://www.gromacs.org/pipermail/gmx-users/2008-August/035543.html).

Which lines did you add, and which did you change to comments in
eigio.c ?

The message from Tsjerk seems pretty clear. You can uncomment lines

110,

111 and 112 in eigio.c and recompile g_anaeig:

make g_anaeig


If everything went fine, you'll get a new executable for g_anaeig,

which

you can then copy to where you had the original version.

Ran.
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

Inon Sharony wrote:
> This is exactly the point - I get only three significant digits.
> Although I performed the entire procedure in double-precision. The
> convergence to 5E-4 DID occur in single-precision, I just thought it
> wasn't good enough (the program recommends 1E-5 and when
> double-precision works for me I got 1E-6 with the files you sent me).
What did you have in the input?
In any case if you get 6 zero frequencies and the rest are positive
you're probably fine.
> I also wouldn't mind a clearer explanation of how you fixed bugzilla
> 168 (see my request at
> http://www.gromacs.org/pipermail/gmx-users/2008-August/035543.html).
> Which lines did you add, and which did you change to comments in
> eigio.c ?
The message from Tsjerk seems pretty clear. You can uncomment lines 110,
111 and 112 in eigio.c and recompile g_anaeig:
>make g_anaeig

If everything went fine, you'll get a new executable for g_anaeig, which
you can then copy to where you had the original version.

Ran.
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

This is exactly the point - I get only three significant digits.  
Although I performed the entire procedure in double-precision. The  
convergence to 5E-4 DID occur in single-precision, I just thought it  
wasn't good enough (the program recommends 1E-5 and when  
double-precision works for me I got 1E-6 with the files you sent me).
I also wouldn't mind a clearer explanation of how you fixed bugzilla  
168 (see my request at  
http://www.gromacs.org/pipermail/gmx-users/2008-August/035543.html).  
Which lines did you add, and which did you change to comments in  
eigio.c ?


Thanks, and have a great week.


Inon.



Quoting "Ran Friedman" <[EMAIL PROTECTED]>:


Hi Inon,

Check the files after EM. How many significant digits do you have?

I

guess you wouldn't get a convergence to 5E-4 with single precision.

From

my experience it may be worth to run several cycles of EM, say CG

and

then L-BFGS to get better convergence.

Ran.


Inon Sharony wrote:

I now performed:

make distclean
./configure --disable-float
make
make install
make links


All executed without problems. Now I no longer have segmentation
faults (thanks David!), however the energy minimization still does

not

achieve 1E-05 kJ / mole nm convergence (only as good as ~5E-04 for
pentane). When I looked in the *.tpr file I saw that the

coordinates

are still given to three significant figures, meaning that the

last

two decimal places (fourth and fifth to the right of the decimal
point) are always zero. I understood from Ran that this means the

data

is still in single-precision. How could this be?

Can anyone please help me get proper, double-precision from my
simulations?


Thanks, and have a glorious week.

Inon.


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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

Hi Inon,

Check the files after EM. How many significant digits do you have? I
guess you wouldn't get a convergence to 5E-4 with single precision. From
my experience it may be worth to run several cycles of EM, say CG and
then L-BFGS to get better convergence.

Ran.


Inon Sharony wrote:
> I now performed:
>
> make distclean
> ./configure --disable-float
> make
> make install
> make links
>
>
> All executed without problems. Now I no longer have segmentation
> faults (thanks David!), however the energy minimization still does not
> achieve 1E-05 kJ / mole nm convergence (only as good as ~5E-04 for
> pentane). When I looked in the *.tpr file I saw that the coordinates
> are still given to three significant figures, meaning that the last
> two decimal places (fourth and fifth to the right of the decimal
> point) are always zero. I understood from Ran that this means the data
> is still in single-precision. How could this be?
>
> Can anyone please help me get proper, double-precision from my
> simulations?
>
>
> Thanks, and have a glorious week.
>
> Inon.

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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

I now performed:

make distclean
./configure --disable-float
make
make install
make links


All executed without problems. Now I no longer have segmentation  
faults (thanks David!), however the energy minimization still does not  
achieve 1E-05 kJ / mole nm convergence (only as good as ~5E-04 for  
pentane). When I looked in the *.tpr file I saw that the coordinates  
are still given to three significant figures, meaning that the last  
two decimal places (fourth and fifth to the right of the decimal  
point) are always zero. I understood from Ran that this means the data  
is still in single-precision. How could this be?


Can anyone please help me get proper, double-precision from my simulations?


Thanks, and have a glorious week.

Inon.


Quoting "David Osguthorpe" <[EMAIL PROTECTED]>:



   Could it be that this, second, compilation might have caused

some

   problems -- I had GROMACS compiled in single-precision, and it

worked

   fine -- could compiling in double-precision after the initial
   single-precision overrun some files? I'm not sure anymore...



from experience if you recompile in a directory from a previous

GROMACS

single precision make you need to do make distclean before

switching

to double
- otherwise you do get random problems such as segfaults/infinite

forces


David
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[David Osguthorpe]

> 
>Could it be that this, second, compilation might have caused some
>problems -- I had GROMACS compiled in single-precision, and it worked
>fine -- could compiling in double-precision after the initial
>single-precision overrun some files? I'm not sure anymore...
> 

from experience if you recompile in a directory from a previous GROMACS
single precision make you need to do make distclean before switching to double
- otherwise you do get random problems such as segfaults/infinite forces

David
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

I think we're getting somewhere...

when I look at the *.tpr file, under the line

nosehoover_xi:  0

I have the x[ 0] etc. lines, but they are as you described single  
precision should look like (the last two digits are all zeros). This  
is despite the fact that at the top it says


Reading file topol.tpr, VERSION 3.3.3 (double precision)

So, when I tried to run the files you sent me (I used the exact  
commands you wrote) I got infinite forces as I usually do.


(Interestingly, for a small molecule (Dichloromethane) I did not get  
segfaults, but also couldn't minimize below a maximal force of about  
1e-3 kJ / mole nm .)


What does this mean?




Thanks

Inon.


Quoting "Ran Friedman" <[EMAIL PROTECTED]>:


Inon Sharony wrote:

Hi Ran.
I looked up your suggestions, and got the following:

0. The parameters in the *.tpr file appear in " 0.e+00 "
format. How can I tell if this is a float or double? Also, I could

not

see if the position coordinates of the molecule appear in the

*.tpr

file (and if so, if they are in double-precision). Where do the
coordinates appear? (in the *.gro file only?)

When you run gmxdump it should right e.g.:
Reading file em.tpr, VERSION 3.3.3 (double precision)

As for the coordinates, you have e.g.:
  x[0]={ 1.35920e+01,  1.80590e+01,  1.79780e+01}
  x[1]={ 1.31410e+01,  1.77710e+01,  1.75260e+01}
  x[2]={ 1.30070e+01,  1.78390e+01,  1.68430e+01}

This is double precision. In single precision you'd get only 3

digits,

and the rest will be zeroes.


1. I do not get any step*.pdb files after the mdrun. In fact, I

skip

the *.pdb file altogether (using PRODRG). Could this be a problem?

It doesn't matter if you use pdb or gro. step*.pdb files are

sometimes

given in the output when the system explodes.

It can be that the parameters from PRODRG are not exactly what you

want

- you should compare with the force field paramters and charges,

though

I'm not sure this can be the source of this behaviour.


2. The simulation is done in vacuo.

3. I examined the input *.gro file (as well as the

single-precision

mdruns) using ngmx, and it looks great for those runs that work

(i.e.,

single precision).


I will now try repeating the whole minimization-NormalMode process

for

a simple diatomic, to see if I have any problems. Could you send a
working set of files for me to compare with? Assuming you've run
Normal Mode analyses in the past...

I'm not sure a diatomic system is good for this - not enough

degrees on

freedom.
I'll send you an example made with GMX 3.2.1 - I'm not doing NMA

too

often, but it should work.



Thanks very much again,

Inon.


Quoting "Ran Friedman" <[EMAIL PROTECTED]>:


Inon Sharony wrote:


 Hi Ran, thanks for the reply

I ran "make tests" after compiling with double precision, and it

came

out fine.

Could it be that this, second, compilation might have caused

some

problems -- I had GROMACS compiled in single-precision, and it

worked

fine -- could compiling in double-precision after the initial
single-precision overrun some files? I'm not sure anymore...

Also, the grompp in double-precision works fine (no warnings,

etc.)

but I get the segfault from mdrun (also in double-precision).
Sometimes this happens in the first minimization step, and

sometimes

in the second. I was told that this might hint that the input

file/s

(e.g. the *.gro file) were input in single- and not

double-precision.

However, since the files have coordinates written in nanometers

to

four significant digits, I can't see how the input numbers could

be in

single or double precision. It was suggested that I insert a

"print to

screen" line in the source code immediately after the *.gro file

is

read, to see if the printed data is in single-precision or
double-precision format. What do you think?


The tpr should contain the data in double precision. You can

check

this

with gmxdump.

Other things that you may want to consider:

1. Do you get step*.pdb files after running mdrun? This may point

out to

something wrong in the input.
2. Are you using a solvated system? Normally NMA is done in

vacuo,

maybe

with some scaling of the dielectric.
3. Did you examine the system that you use in the input? Does it

make

sense to you?

Ran.
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

Ran Friedman wrote:
> Inon Sharony wrote:
>   
>> Hi Ran.
>> I looked up your suggestions, and got the following:
>>
>> 0. The parameters in the *.tpr file appear in " 0.e+00 "
>> format. How can I tell if this is a float or double? Also, I could not
>> see if the position coordinates of the molecule appear in the *.tpr
>> file (and if so, if they are in double-precision). Where do the
>> coordinates appear? (in the *.gro file only?)
>> 
> When you run gmxdump it should right e.g.:
>   
correction: Should WRITE.
> Reading file em.tpr, VERSION 3.3.3 (double precision)
>
> As for the coordinates, you have e.g.:
>   x[0]={ 1.35920e+01,  1.80590e+01,  1.79780e+01}
>   x[1]={ 1.31410e+01,  1.77710e+01,  1.75260e+01}
>   x[2]={ 1.30070e+01,  1.78390e+01,  1.68430e+01}
>
> This is double precision. In single precision you'd get only 3 digits,
> and the rest will be zeroes.
>   
>> 1. I do not get any step*.pdb files after the mdrun. In fact, I skip
>> the *.pdb file altogether (using PRODRG). Could this be a problem?
>> 
> It doesn't matter if you use pdb or gro. step*.pdb files are sometimes
> given in the output when the system explodes.
>
> It can be that the parameters from PRODRG are not exactly what you want
> - you should compare with the force field paramters and charges, though
> I'm not sure this can be the source of this behaviour.
>   
>> 2. The simulation is done in vacuo.
>>
>> 3. I examined the input *.gro file (as well as the single-precision
>> mdruns) using ngmx, and it looks great for those runs that work (i.e.,
>> single precision).
>>
>>
>> I will now try repeating the whole minimization-NormalMode process for
>> a simple diatomic, to see if I have any problems. Could you send a
>> working set of files for me to compare with? Assuming you've run
>> Normal Mode analyses in the past...
>> 
> I'm not sure a diatomic system is good for this - not enough degrees on
> freedom.
> I'll send you an example made with GMX 3.2.1 - I'm not doing NMA too
> often, but it should work.
>   
>> Thanks very much again,
>>
>> Inon.
>>
>>
>> Quoting "Ran Friedman" <[EMAIL PROTECTED]>:
>>
>> 
>>> Inon Sharony wrote:
>>>   
  Hi Ran, thanks for the reply

 I ran "make tests" after compiling with double precision, and it
 
>> came
>> 
 out fine.

 Could it be that this, second, compilation might have caused some
 problems -- I had GROMACS compiled in single-precision, and it
 
>> worked
>> 
 fine -- could compiling in double-precision after the initial
 single-precision overrun some files? I'm not sure anymore...

 Also, the grompp in double-precision works fine (no warnings,
 
>> etc.)
>> 
 but I get the segfault from mdrun (also in double-precision).
 Sometimes this happens in the first minimization step, and
 
>> sometimes
>> 
 in the second. I was told that this might hint that the input
 
>> file/s
>> 
 (e.g. the *.gro file) were input in single- and not
 
>> double-precision.
>> 
 However, since the files have coordinates written in nanometers to
 four significant digits, I can't see how the input numbers could
 
>> be in
>> 
 single or double precision. It was suggested that I insert a
 
>> "print to
>> 
 screen" line in the source code immediately after the *.gro file
 
>> is
>> 
 read, to see if the printed data is in single-precision or
 double-precision format. What do you think?

 
>>> The tpr should contain the data in double precision. You can check
>>>   
>> this
>> 
>>> with gmxdump.
>>>
>>> Other things that you may want to consider:
>>>
>>> 1. Do you get step*.pdb files after running mdrun? This may point
>>>   
>> out to
>> 
>>> something wrong in the input.
>>> 2. Are you using a solvated system? Normally NMA is done in vacuo,
>>>   
>> maybe
>> 
>>> with some scaling of the dielectric.
>>> 3. Did you examine the system that you use in the input? Does it
>>>   
>> make
>> 
>>> sense to you?
>>>
>>> Ran.
>>> ___
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>>>
>>>   
>> --Inon   Sharony
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

Inon Sharony wrote:
> Hi Ran.
> I looked up your suggestions, and got the following:
>
> 0. The parameters in the *.tpr file appear in " 0.e+00 "
> format. How can I tell if this is a float or double? Also, I could not
> see if the position coordinates of the molecule appear in the *.tpr
> file (and if so, if they are in double-precision). Where do the
> coordinates appear? (in the *.gro file only?)
When you run gmxdump it should right e.g.:
Reading file em.tpr, VERSION 3.3.3 (double precision)

As for the coordinates, you have e.g.:
  x[0]={ 1.35920e+01,  1.80590e+01,  1.79780e+01}
  x[1]={ 1.31410e+01,  1.77710e+01,  1.75260e+01}
  x[2]={ 1.30070e+01,  1.78390e+01,  1.68430e+01}

This is double precision. In single precision you'd get only 3 digits,
and the rest will be zeroes.
>
> 1. I do not get any step*.pdb files after the mdrun. In fact, I skip
> the *.pdb file altogether (using PRODRG). Could this be a problem?
It doesn't matter if you use pdb or gro. step*.pdb files are sometimes
given in the output when the system explodes.

It can be that the parameters from PRODRG are not exactly what you want
- you should compare with the force field paramters and charges, though
I'm not sure this can be the source of this behaviour.
>
> 2. The simulation is done in vacuo.
>
> 3. I examined the input *.gro file (as well as the single-precision
> mdruns) using ngmx, and it looks great for those runs that work (i.e.,
> single precision).
>
>
> I will now try repeating the whole minimization-NormalMode process for
> a simple diatomic, to see if I have any problems. Could you send a
> working set of files for me to compare with? Assuming you've run
> Normal Mode analyses in the past...
I'm not sure a diatomic system is good for this - not enough degrees on
freedom.
I'll send you an example made with GMX 3.2.1 - I'm not doing NMA too
often, but it should work.
>
>
> Thanks very much again,
>
> Inon.
>
>
> Quoting "Ran Friedman" <[EMAIL PROTECTED]>:
>
>> Inon Sharony wrote:
>>>
>>>  Hi Ran, thanks for the reply
>>>
>>> I ran "make tests" after compiling with double precision, and it
> came
>>> out fine.
>>>
>>> Could it be that this, second, compilation might have caused some
>>> problems -- I had GROMACS compiled in single-precision, and it
> worked
>>> fine -- could compiling in double-precision after the initial
>>> single-precision overrun some files? I'm not sure anymore...
>>>
>>> Also, the grompp in double-precision works fine (no warnings,
> etc.)
>>> but I get the segfault from mdrun (also in double-precision).
>>> Sometimes this happens in the first minimization step, and
> sometimes
>>> in the second. I was told that this might hint that the input
> file/s
>>> (e.g. the *.gro file) were input in single- and not
> double-precision.
>>> However, since the files have coordinates written in nanometers to
>>> four significant digits, I can't see how the input numbers could
> be in
>>> single or double precision. It was suggested that I insert a
> "print to
>>> screen" line in the source code immediately after the *.gro file
> is
>>> read, to see if the printed data is in single-precision or
>>> double-precision format. What do you think?
>>>
>> The tpr should contain the data in double precision. You can check
> this
>> with gmxdump.
>>
>> Other things that you may want to consider:
>>
>> 1. Do you get step*.pdb files after running mdrun? This may point
> out to
>> something wrong in the input.
>> 2. Are you using a solvated system? Normally NMA is done in vacuo,
> maybe
>> with some scaling of the dielectric.
>> 3. Did you examine the system that you use in the input? Does it
> make
>> sense to you?
>>
>> Ran.
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

Hi Ran.
I looked up your suggestions, and got the following:

0. The parameters in the *.tpr file appear in " 0.e+00 "  
format. How can I tell if this is a float or double? Also, I could not  
see if the position coordinates of the molecule appear in the *.tpr  
file (and if so, if they are in double-precision). Where do the  
coordinates appear? (in the *.gro file only?)


1. I do not get any step*.pdb files after the mdrun. In fact, I skip  
the *.pdb file altogether (using PRODRG). Could this be a problem?


2. The simulation is done in vacuo.

3. I examined the input *.gro file (as well as the single-precision  
mdruns) using ngmx, and it looks great for those runs that work (i.e.,  
single precision).



I will now try repeating the whole minimization-NormalMode process for  
a simple diatomic, to see if I have any problems. Could you send a  
working set of files for me to compare with? Assuming you've run  
Normal Mode analyses in the past...



Thanks very much again,

Inon.


Quoting "Ran Friedman" <[EMAIL PROTECTED]>:


Inon Sharony wrote:


 Hi Ran, thanks for the reply

I ran "make tests" after compiling with double precision, and it

came

out fine.

Could it be that this, second, compilation might have caused some
problems -- I had GROMACS compiled in single-precision, and it

worked

fine -- could compiling in double-precision after the initial
single-precision overrun some files? I'm not sure anymore...

Also, the grompp in double-precision works fine (no warnings,

etc.)

but I get the segfault from mdrun (also in double-precision).
Sometimes this happens in the first minimization step, and

sometimes

in the second. I was told that this might hint that the input

file/s

(e.g. the *.gro file) were input in single- and not

double-precision.

However, since the files have coordinates written in nanometers to
four significant digits, I can't see how the input numbers could

be in

single or double precision. It was suggested that I insert a

"print to

screen" line in the source code immediately after the *.gro file

is

read, to see if the printed data is in single-precision or
double-precision format. What do you think?


The tpr should contain the data in double precision. You can check

this

with gmxdump.

Other things that you may want to consider:

1. Do you get step*.pdb files after running mdrun? This may point

out to

something wrong in the input.
2. Are you using a solvated system? Normally NMA is done in vacuo,

maybe

with some scaling of the dielectric.
3. Did you examine the system that you use in the input? Does it

make

sense to you?

Ran.
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

Inon Sharony wrote:
>
>  Hi Ran, thanks for the reply
>
> I ran "make tests" after compiling with double precision, and it came
> out fine.
>
> Could it be that this, second, compilation might have caused some
> problems -- I had GROMACS compiled in single-precision, and it worked
> fine -- could compiling in double-precision after the initial
> single-precision overrun some files? I'm not sure anymore...
>
> Also, the grompp in double-precision works fine (no warnings, etc.)
> but I get the segfault from mdrun (also in double-precision).
> Sometimes this happens in the first minimization step, and sometimes
> in the second. I was told that this might hint that the input file/s
> (e.g. the *.gro file) were input in single- and not double-precision.
> However, since the files have coordinates written in nanometers to
> four significant digits, I can't see how the input numbers could be in
> single or double precision. It was suggested that I insert a "print to
> screen" line in the source code immediately after the *.gro file is
> read, to see if the printed data is in single-precision or
> double-precision format. What do you think?
>
The tpr should contain the data in double precision. You can check this
with gmxdump.

Other things that you may want to consider:

1. Do you get step*.pdb files after running mdrun? This may point out to
something wrong in the input.
2. Are you using a solvated system? Normally NMA is done in vacuo, maybe
with some scaling of the dielectric.
3. Did you examine the system that you use in the input? Does it make
sense to you?

Ran.
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[gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

 Hi Ran, thanks for the reply 

I ran "make tests" after compiling with double precision, and it came out fine. 

Could it be that this, second, compilation might have caused some problems -- I 
had GROMACS compiled in single-precision, and it worked fine -- could compiling 
in double-precision after the initial single-precision overrun some files? I'm 
not sure anymore... 

Also, the grompp in double-precision works fine (no warnings, etc.) but I get 
the segfault from mdrun (also in double-precision). Sometimes this happens in 
the first minimization step, and sometimes in the second. I was told that this 
might hint that the input file/s (e.g. the *.gro file) were input in single- 
and not double-precision. However, since the files have coordinates written in 
nanometers to four significant digits, I can't see how the input numbers could 
be in single or double precision. It was suggested that I insert a "print to 
screen" line in the source code immediately after the *.gro file is read, to 
see if the printed data is in single-precision or double-precision format. What 
do you think? 

Thanks again, everyone

-- 
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Re: [gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

Hi,

It's hard to know why you get a segmentation fault without further info.
Did you ran the GMX tests after installation with double precision? Is
everything all right there?

Also, when exactly the system crashes? Is it straight when you start
mdrun? Did you use both grompp and mdrun in double precision?

Good luck,
Ran.

Inon Sharony wrote:
> Hi all!
>
> I'm trying to perform a normal mode (NM) analysis, but having trouble
> with the
> recommendation of first performing a double precision energy
> minimization before writing
> the Hessian. The calculation of the Hessian matrix is done using
> mdrun, and its
> diagonalization is done using g_nmeig. I have managed this procedure
> using single-precision, but if the recommended maximal force (the
> minimization convergence criterion) is 1E-5 kJ mole^-1 nm^-1 , I was
> only able so far to get to 1E-2 before getting a message that the
> minimization algorithm has reached machine precision. I have tried
> Conjugate Gradient and L-BFGS.
>
> I also compiled GROMACS in double-precision, but for some reason when
> I try to minimize the energy of the same molecules, I get a
> segmentation fault. I'm not sure where this is coming from (already
> checked the user lists).
>
> Can someone with experience in Normal Mode analysis in GROMACS (or
> just general
> experience in using GROMACS with double-precision) help me with my
> difficulty?
>
> (Currently I'm running pentane or para-dimethylbenzene)
>
> Thanks for your help,
> --Inon   Sharony
> ×™× ×•×Ÿ ×©×¨×•× ×™
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing
> this e-mail.
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>


-- 
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: [EMAIL PROTECTED]
Skype: ran.friedman
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[gmx-users] Normal Mode Analysis in Double-Precision

[Inon Sharony]

Hi all!

I'm trying to perform a normal mode (NM) analysis, but having trouble with the
recommendation of first performing a double precision energy  
minimization before writing
the Hessian. The calculation of the Hessian matrix is done using  
mdrun, and its
diagonalization is done using g_nmeig. I have managed this procedure  
using single-precision, but if the recommended maximal force (the  
minimization convergence criterion) is 1E-5 kJ mole^-1 nm^-1 , I was  
only able so far to get to 1E-2 before getting a message that the  
minimization algorithm has reached machine precision. I have tried  
Conjugate Gradient and L-BFGS.


I also compiled GROMACS in double-precision, but for some reason when  
I try to minimize the energy of the same molecules, I get a  
segmentation fault. I'm not sure where this is coming from (already  
checked the user lists).


Can someone with experience in Normal Mode analysis in GROMACS (or  
just general

experience in using GROMACS with double-precision) help me with my difficulty?

(Currently I'm running pentane or para-dimethylbenzene)

Thanks for your help,
--
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Re: [gmx-users] normal mode analysis

[Bert de Groot]

Robert Fenwick wrote:
> 
> 
> Hi,
> 
> I am interested in comparing the normal modes of a protein with and
> without a ligand. I have already computed the lowest 100 normal modes
> for the protein (eigenvec_a.trr) and the protein:ligand complex and have
> reduced the protein:ligand eigenvec_b.trr to the protein by issuing;
> 
>> trjconv_d -f eigenvec_b.trr -o eigenvec_c.trr -s nm_a.tpr
>> select 0 [System]
> 
> Where:
> + nm_a.tpr is the tpr file of the protein alone
> + eigenvec_b.trr is the trajectory of the protein:ligand
> + eigenvec_c.trr is the new trajectory of the complex minus the ligand
> coordinates
> 
> What I want to do now is compare the eigenvec_a.trr and eigenvec_c.trr
> files to see the mode overlap between the free and bound protein.
> 
> What I can not understand how to remove the effects of rotation and
> translation of the protein with respect to the ligand that will be
> present in the eigenvec_c.trr. Is it possible to do this type of
> analysis in GROMACS and how can I go about it?
> 


if you remove part of the system e.g. the ligand) from a set of eigenvectors
you'll end up with non-orthogonal vectors. This is almost certainly not what you
want.

I'd suggest for each set of normal modes (with and without ligand) to generate a
corresponding ensemble at a certain temperature with g_nmens. Then from those
trajectories you can cut out the ligand to generate two protein-only
trajectories, on which you then can run a PCA with g_covar (either separately
and calculate eigenvector overlaps, or concatenate both trajectories and look at
projection differences).

best,

Bert

__
Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302
http://www.mpibpc.mpg.de/groups/de_groot
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Re: [gmx-users] normal mode analysis

[Florian Haberl]

Hi, 

On Friday, 21. December 2007 12:48, Robert Fenwick wrote:
> Hi,
>
> I am interested in comparing the normal modes of a protein with and
> without a ligand. I have already computed the lowest 100 normal modes
> for the protein (eigenvec_a.trr) and the protein:ligand complex and
> have reduced the protein:ligand eigenvec_b.trr to the protein by
> issuing;
>
>  > trjconv_d -f eigenvec_b.trr -o eigenvec_c.trr -s nm_a.tpr
>  > select 0 [System]
>
> Where:
> + nm_a.tpr is the tpr file of the protein alone
> + eigenvec_b.trr is the trajectory of the protein:ligand
> + eigenvec_c.trr is the new trajectory of the complex minus the
> ligand coordinates
>
> What I want to do now is compare the eigenvec_a.trr and
> eigenvec_c.trr files to see the mode overlap between the free and
> bound protein.
>
> What I can not understand how to remove the effects of rotation and
> translation of the protein with respect to the ligand that will be
> present in the eigenvec_c.trr. Is it possible to do this type of
> analysis in GROMACS and how can I go about it?

Fit it first on the same reference structure, i think CA or Backbone atoms are 
enough for this kind of analysis.

g_covar -h (calculating the covariance matrix)
and
g_anaeig -h -inpr (compare the different systems)
should help you 
you can only compare matrix/ trajectories with the same atom number.


>
> Regards,
>
>
> Bryn
>
>
>  ==
>  R. Bryn FenwickDepartment of Biochemistry,
>  [EMAIL PROTECTED]University of Cambridge,
>  [EMAIL PROTECTED]80 Tennis Court Road,
>  Tel: +44 1223 766018   Old Addenbrookes Site,
>  Fax: +44 1223 766002   Cambridge, CB2 1GA, UK.
>  ==
>
>
>
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Greetings,

Florian

-- 
---
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[gmx-users] normal mode analysis

[Robert Fenwick]

Hi,

I am interested in comparing the normal modes of a protein with and  
without a ligand. I have already computed the lowest 100 normal modes  
for the protein (eigenvec_a.trr) and the protein:ligand complex and  
have reduced the protein:ligand eigenvec_b.trr to the protein by  
issuing;


> trjconv_d -f eigenvec_b.trr -o eigenvec_c.trr -s nm_a.tpr
> select 0 [System]

Where:
+ nm_a.tpr is the tpr file of the protein alone
+ eigenvec_b.trr is the trajectory of the protein:ligand
+ eigenvec_c.trr is the new trajectory of the complex minus the  
ligand coordinates


What I want to do now is compare the eigenvec_a.trr and  
eigenvec_c.trr files to see the mode overlap between the free and  
bound protein.


What I can not understand how to remove the effects of rotation and  
translation of the protein with respect to the ligand that will be  
present in the eigenvec_c.trr. Is it possible to do this type of  
analysis in GROMACS and how can I go about it?


Regards,


Bryn


==
R. Bryn FenwickDepartment of Biochemistry,
[EMAIL PROTECTED]University of Cambridge,
[EMAIL PROTECTED]80 Tennis Court Road,
Tel: +44 1223 766018   Old Addenbrookes Site,
Fax: +44 1223 766002   Cambridge, CB2 1GA, UK.
==



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Re: [gmx-users] Normal Mode Analysis

[Erik Lindahl]

Hi,

First, it's just a warning that the force _might_ not be small enough  
since there's no bullet-proof way to say.


In general, both for final-stage energy minimization (with L-BFGS)  
and actual normal mode analysis you can use a setup with


double precision
switched coulomb & vdw interactions; cutoffs e.g. at 1.0 nm, switched  
from 0.8 nm (or shifted from 0 nm).

rlist at 1.2 to 1.3

It is imperative that you use the -t option to grompp when you create  
the NM run input file, so you read full precision binary coordinates  
and not the three-decimal gro file.


Cheers,

Erik

On Jul 4, 2007, at 8:37 AM, Anirban Ghosh wrote:


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Re: [gmx-users] normal mode analysis (size issue)

[Erik Lindahl]

Hi,

On Jun 19, 2007, at 5:26 PM, Liwei Li wrote:

I want to carry out normal mode analysis on a large protein (about  
10,000 atoms) without using coarse grain approximations. Amber is  
out of the question since it can only handle about 5,000 atoms for  
NMA. I am wondering if GROMACS can deal with this assuming running  
on a 64-bit machine with 8G memory. I truely appreciate it if you  
can help.




If you use release 3.3 or later you won't even need lots of memory  
since we're using sparse matrix representation and diagonalization as  
soon as you have cutoffs, which should always be the case if you're  
doing NMA in vacuo.


We regularly do such NMA on 25,000-atom systems.

The best interaction form is usually shifted interactions with a  
cutoff of 1.2 to 1.4 nm. First minimize with steepest descent, then  
_double_ precision l-bfgs. This is virtually the only case when you  
absolutely need double precision. The rlist variable should be  
~0.2-0.3nm larger to conserve energy with l-bfgs, since that helps  
convergence.


Cheers,

Erik





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[gmx-users] normal mode analysis (size issue)

[Liwei Li]

Hi,

I want to carry out normal mode analysis on a large protein (about 10,000
atoms) without using coarse grain approximations. Amber is out of the
question since it can only handle about 5,000 atoms for NMA. I am wondering
if GROMACS can deal with this assuming running on a 64-bit machine with 8G
memory. I truely appreciate it if you can help.


Liwei Li
Postdoctoral Associate
Department of Biochemistry,
Indiana University School of Medicine,
410 W. 10th Street, Suite 5000
Indianaposlis, IN 46202
Tel: (317)278-9185
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Re: [gmx-users] Normal mode analysis - reference [34] in the Gromacs manual

[David van der Spoel]

Ran Friedman wrote:

It seems like reference #34 in the GMX 3.3 manual should be:

Levitt, M., Sander, C. and Stern PS. The normal modes of a protein: native
bovine pancreatic trypsin inhibitor. Internatl. J. Quant.Chem., Quantum 
Biology

Symposium 10, 181-199. 1983

And not as written.
Ran.


thanks, I fixed it.

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Normal mode analysis - reference [34] in the Gromacs manual

[Ran Friedman]

It seems like reference #34 in the GMX 3.3 manual should be:

Levitt, M., Sander, C. and Stern PS. The normal modes of a protein: native
bovine pancreatic trypsin inhibitor. Internatl. J. Quant.Chem., Quantum Biology
Symposium 10, 181-199. 1983

And not as written.
Ran.

--
--
Ran Friedman
http://bioinfo.tau.ac.il/~ran
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
--

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