Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin

[toma0052]

Hello,
It looks like the problem might be in my mdp settings. I am using the 
MARTINI force field which uses shift functions for both electrostatics and 
vdw which are only available in the group-based cut-off scheme. OpenMP 
doesn't seem to run with the group-based cut-off scheme, just Verlet.
If I switch the cut-off scheme to Verlet and change the vdw and 
coulombtype to cut-off and then add in potential-shift-verlet as modifiers 
I can get the system to run. However, in doing this, am I mucking up the 
force field?


Thanks,
Mike


On Feb 26 2013, Mirco Wahab wrote:


Hi Mike

On 25.02.2013 17:25, toma0...@umn.edu wrote:

...
Estimated maximum distance required for P-LINCS: 0.810 nm
...
Domain decomposition grid 4 x 2 x 1, separate PME nodes 0


Do your runs use PME and/or P-LINCS?

Maybe you could point out the problem by disabling
each or both in yout .mdp file?

I tested some systems (without PME) on cygwin/gmx
4.6 that worked ok. Probably glitches with the
cygwin-provided fftw3?

Maybe you could try to compile fftwf 3.3.3
in single precision from source and link it to
your gromacs build.
 
http://www.fftw.org/fftw3_doc/Installation-on-Unix.html#Installation-on-Unix




M.



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Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin

[toma0052]

Hi,
I have run the 3 scenarios that you mentioned. The commands and output 
are pasted below.


Thanks,
Mike


***Trial 1***
mdrun -v -deffnm Clp_Test -ntmpi 1 -ntomp 1
Reading file Clp_Test.tpr, VERSION 4.6 (single precision)
Using 1 MPI thread

Can not set thread affinities on the current platform. On NUMA systems this
can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers.

starting mdrun 'Martini system for ClpX'
1 steps,200.0 ps.

--Relavant outpur from log file--
Log file opened on Mon Feb 25 20:26:57 2013
Host: Theory-Monster  pid: 8176  nodeid: 0  nnodes:  1
Gromacs version:VERSION 4.6
Precision:  single
Memory model:   32 bit
MPI library:thread_mpi
OpenMP support: enabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.3-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Mon, Feb 25, 2013 10:38:04 AM
Built by:   Mike@Theory-Monster [CMAKE]
Build OS/arch:  CYGWIN_NT-6.1-WOW64 1.7.17(0.262/5/3) i686
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
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 s

se4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/gcc.exe GNU gcc (GCC) 4.5.3
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers 
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer

-funroll-all-loops -fexcess-precision=fast  -O3 -DNDEBUG

Using 1 MPI thread

Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Family:  6  Model: 45  Stepping:  7
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
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256

Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's:   NS: 1.4   Coulomb: 1.2   LJ: 1.2
System total charge: 0.000
Generated table with 1200 data points for Shift.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ12Shift.
Tabscale = 500 points/nm
Potential shift: LJ r^-12: 0.000 r^-6 0.000
Removing pbc first time

Can not set thread affinities on the current platform. On NUMA systems this
can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers.

Initializing LINear Constraint Solver

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
  --- Thank You ---  

The number of constraints is 840
414 constraints are involved in constraint triangles,
will apply an additional matrix expansion of order 4 for couplings
between constraints inside triangles
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
 0:  rest

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
  --- Thank You ---  


***Trial 2***
mdrun -v -deffnm Clp_Test -ntmpi 1
Reading file Clp_Test.tpr, VERSION 4.6 (single precision)
Using 1 MPI thread

Can not set thread affinities on the current platform. On NUMA systems this
can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers.
starting mdrun 'Martini system for ClpX'
1 steps,200.0 ps.

--Relavant outpur from log file--
Log file opened on Mon Feb 25 20:40:32 2013
Host: Theory-Monster  pid: 4624  nodeid: 0  nnodes:  1
Gromacs version:VERSION 4.6
Precision:  single
Memory model:   32 bit
MPI library:thread_mpi
OpenMP support: enabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.3-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Mon, Feb 25, 2013 10:38:04 AM
Built by:   Mike@Theory-Monster [CMAKE]
Build OS/arch:  CYGWIN_NT-6.1-WOW64 1.7.17(0.262/5/3) i686
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Build CPU family:   6   Model: 45   Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt 

[gmx-users] Re: Gromacs 4.6 Installation under Cygwin

[toma0052]

Hello,
Thanks for the help. After setting the library path properly, I seem 
to be able to get gromacs up and running. However, I have run into another 
problem with mdrun and actually running any jobs. When I execute
mdrun -v -deffnm Clp_Test -nt 


The output is: Reading file Clp_Test.tpr, VERSION 4.6 (single precision)
Using 8 MPI threads

Followed by several occurrences of:
Can not set thread affinities on the current platform. On NUMA systems this
can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers.

Then:
starting mdrun 'Martini system for ClpX'
1 steps,200.0 ps.

After this however, the simulation never actually begins. I can get rid of 
the error messages by using -pin off, but that doesn't seem to actually fix 
anything. Is there something that has not been installed properly? Below is 
the seemingly relevant portions of the log file generated by the above 
mdrun command.



Log file opened on Mon Feb 25 11:21:08 2013
Host: Theory-Monster  pid: 3192  nodeid: 0  nnodes:  1
Gromacs version:VERSION 4.6
Precision:  single
Memory model:   32 bit
MPI library:thread_mpi
OpenMP support: enabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.3-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Mon, Feb 25, 2013 10:38:04 AM
Built by:   Mike@Theory-Monster [CMAKE]
Build OS/arch:  CYGWIN_NT-6.1-WOW64 1.7.17(0.262/5/3) i686
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
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: /usr/bin/gcc.exe GNU gcc (GCC) 4.5.3
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers 
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer 
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG


Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
   two-body bonded interactions: 0.988 nm, Bond, atoms 997 1005
 multi-body bonded interactions: 1.042 nm, G96Angle, atoms 1938 1942
Minimum cell size due to bonded interactions: 1.146 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.810 nm
Estimated maximum distance required for P-LINCS: 0.810 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 1.433 nm
The maximum allowed number of cells is: X 11 Y 11 Z 9
Domain decomposition grid 4 x 2 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0

Using 8 MPI threads

Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Family:  6  Model: 45  Stepping:  7
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

Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256

Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's:   NS: 1.4   Coulomb: 1.2   LJ: 1.2
System total charge: 0.000
Generated table with 1200 data points for Shift.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ12Shift.
Tabscale = 500 points/nm
Potential shift: LJ r^-12: 0.000 r^-6 0.000
Removing pbc first time

Can not set thread affinities on the current platform. On NUMA systems this
can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers.

Initializing Parallel LINear Constraint Solver

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
  --- Thank You ---  

The number of constraints is 840
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration
414 constraints are involved in constraint triangles,
will apply an additional matrix expansion of order 4 for couplings
between constraints inside triangles

Linking all bonded interactions to atoms

The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 4.02 nm Y 8.04 nm

The maximum allowed distance for charge groups involved in interactions is:
non-bonded inter

[gmx-users] Gromacs 4.6 Installation under Cygwin

[toma0052]

Hello,
I am trying to install Gromacs 4.6 on a Windows workstation under 
cygwin. After I install everything, when executing g_luck I come up with 
the error:
'error while loading shared libraries: cyggmx-6.dll: cannot open shared 
object file: No such file or directory'
There does exist the file cyggmx-6.dll in /usr/local/gromacs/lib and I 
have tried: export LD_LIBRARY_PATH=/usr/local/gromacs/lib as well as using 
the flag -BUILD_SHARED_LIBS=OFF with cmake, but neither seem to help. What 
could be the cause of this?


Thanks,
Mike
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Re: [gmx-users] 4.5.3 Installation under Cygwin

[toma0052]

Thanks for the response. I tried building gromacs using cmake and the 
procedure from the wiki. Are there custom flags that I have to pass to 
cmake for it to work under cygwin? The cmake procedure seems to run fine 
without any errors, but I cannot evoke any gromacs tool following 
installation. I get the error:

$ g_energy -h
/usr/local/gromacs/bin/g_energy.exe: error while loading shared libraries: 
cyggmxana-6.dll: cannot open shared object file: No such file or directory


I found info on the mailing list related to the absence of DLLs, but the 
fix seemed to be applied to version 3.3.3



Is there something I am missing?

Thanks,
Mike


On Jan 31 2011, Mark Abraham wrote:




On 01/31/11, toma0...@umn.edu wrote:

Hello,
      I am trying to install gromacs 4.5.3 on my desktop under Cygwin. 
Using the installation procedure from the Wiki:
   
(

Install fftw-3.2.2 with ./configure --enable-sse --enable-float
make
make install

Then install gromacs with:
./configure --enable-shared LDFLAGS='-L/usr/local/lib'
make

  The installation fails here with many errors not being able to find 
libraries associated with fftw tracing back to this error:


  *** Warning: This system can not link to static lib archive 
/usr/local/lib/libfftw3f.la.

*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have.

  The installation procedure from the Wiki works fine with gromacs-4.0.7. 
This error only occurs with the 4.5 series. Are there different default 
settings for where gromacs looks for fftw between 4.0.7 and 4.5.3? Any help 
would be appreciated.




I ran into the same issue a while back. I don't know what causes it. I 
found that using a CMake-based build on Cygwin worked.


Mark


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[gmx-users] 4.5.3 Installation under Cygwin

[toma0052]

Hello,
I am trying to install gromacs 4.5.3 on my desktop under Cygwin. Using 
the installation procedure from the Wiki:

(
Install fftw-3.2.2 with 
./configure --enable-sse --enable-float

make
make install

Then install gromacs with:
./configure --enable-shared LDFLAGS='-L/usr/local/lib'
make

The installation fails here with many errors not being able to find 
libraries associated with fftw tracing back to this error:


*** Warning: This system can not link to static lib archive 
/usr/local/lib/libfftw3f.la.

*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have.

The installation procedure from the Wiki works fine with gromacs-4.0.7. 
This error only occurs with the 4.5 series. Are there different default 
settings for where gromacs looks for fftw between 4.0.7 and 4.5.3? Any help 
would be appreciated.


Thanks,
Mike
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Re: [gmx-users] g_clustsize output

[toma0052]

Hello,
Thanks for the response. g_clustsize outputs two xpm files of the 
weighted and non-weighted cluster size vs time. Is there another way for me 
to get number of clusters vs cluster size?


Thanks,
Mike



On May 20 2010, David van der Spoel wrote:


On 2010-05-20 04.55, toma0...@umn.edu wrote:

Hello,
I have a system of dimers which spontaneously assemble into clusters. I
would like to get a plot of the number of clusters of size s vs s. In
looking at g_clustsize I am able to obtain the average number of
clusters vs time, the average cluster size vs time and a histogram of
the average number of molecules in a cluster of size s. Am I missing
something? Is there a way for me to get the number of clusters of a
particular size vs cluster size?

Thanks,
Mike Tomasini
g_clustsize will make an xpm plot for this as well, IIRC it is called 
csize.xpm. You can turn it into eps using xpm2ps.





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[gmx-users] g_clustsize output

[toma0052]

Hello,
I have a system of dimers which spontaneously assemble into clusters. 
I would like to get a plot of the number of clusters of size s vs s. In 
looking at g_clustsize I am able to obtain the average number of clusters 
vs time, the average cluster size vs time and a histogram of the average 
number of molecules in a cluster of size s. Am I missing something? Is 
there a way for me to get the number of clusters of a particular size vs 
cluster size?


Thanks,
Mike Tomasini
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[gmx-users] pbc with nwall = 1

[toma0052]

Hello,
I want to study polymer adsorption onto a surface. To do so, I create 
a polymer-solvent system with a wall at z = 0 and use pbc = xy. This, 
however makes the system infinite in the z-direction. I was wondering if 
there was a way to create a periodic boundary at z = L such that when an 
atom crosses z = L the z-coordinate shifts to z = L/2 (rather than z=0 in 
normal pbc) but not the other way around. In this way I could have a 
portion of my system near the surface and a portion far from the surface 
which would represent the bulk. Is this possible? Would it require 
substantial modification to the code?


Thanks,
Mike
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[gmx-users] Position restraints on a lipid bilayer

[toma0052]

Hello,
 I am looking to add position restraints to some atoms of a lipid
bilayer.  There seem to be a lot in the list archives on this subject, but I
am still a tad confused.  What I would like to do is to position restrain the
phosphorus atoms in only one leaflet of the bilayer.  So how do I generate
such a pr file, and where should I include it?  It seems as if things are
done per molecule, so if I put it in my *.top or *.itp files, the restraint
is on all P atoms in the system, not just the ones I want.  Is there a way to
do this so that things are indexed per atom rather than per molecule?

Thanks,
Mike


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[gmx-users] Dextran Simulations

[toma0052]

Hello,
 I would like to simulate the glucose polymer dextran (~5-10 subunits)
and I am wondering what is the best way to do go about doing this.  In
looking at ffgmx.rtp I see GLCA/B which seem to be the glucose parameter
files.  If my numbering scheme is correct, to produce a linear dextran
molecule I want alpha(1-6) linkages, or alpha(1-4) linkages for a branched
polymer which would correspond to O6-C1 and O3-C1 respectively.  However, in
the .rtp file, these bonds are not given, only O4-C1 and O2-C1 are included. 
Is my numbering off, or is there another way to do this?
 I have tried the PRODRG server to create these molecules, and it seemed
to work alright, but I am still a little skeptical about the output.  The
charges appear to be different than in the ffgmx.
 I understand that ffgmx is depreciated, which leads to me second
question (Maybe this should be a different thread).  I would like,
eventually, to look at the different dextran polymers interacting with a DPPC
bilayer.  For the lipids, I am using those of Dr. P. Tieleman in which my
dppc.top file includes ffgmx.itp which is why I am looking at this force
field for the dextran.  If ffgmx is not a force field to use, what would be
better for simulating lipids and carbohydrates?  ffG43a2x?  I have read for
protein simulations people using the Berger lipids and OPLS-AA, would it be
fair to extend this to lipids and carbohydrates?


Thanks,
Mike Tomasini

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[gmx-users] grompp not recognizing mdp file parameters

[toma0052]

Hello,
 It seems that I am having a problem in that grompp is not recognizing
the parameters that I enter into an mdp file, nor is it recognizing the text
in the .top file.  When I run a simulation, the output that I get is as
follows:

ERROR: invalid enum 'md' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
ERROR: invalid enum 'grid' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
ERROR: invalid enum 'xyz' for variable pbc, using 'xyz'
Next time use one of: 'xyz' 'no' 'full'
ERROR: invalid enum 'PME' for variable coulombtype, using 'Cut-off'
Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field'
'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-Born'
'Reaction-Field-nec' 'Encad-shift' 'PME-User'
ERROR: invalid enum 'yes' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
ERROR: invalid enum 'berendsen' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'
ERROR: invalid enum 'berendsen' for variable Pcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'
ERROR: invalid enum 'Semiisotropic' for variable Pcoupltype, using
'Isotropic'
Next time use one of: 'Isotropic' 'Semiisotropic' 'Anisotropic'
'Surface-Tension'
ERROR: invalid enum 'all-bonds' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
checking input for internal consistency...
sh: /lib/cpp: No such file or directory
processing coordinates...
---
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (area_1.03_1.gro, 17365)
 does not match topology (dppc.top, 0)
---

 What could be the problem here?  Is this just some simple formatting
error that I've missed?  I have run simulations before, and everything seemed
to work out fine.  The run above is simply the same files from the successful
simulation copied into a new directory with a few alterations made to the mdp
file.  If my other files still run, why are essentially the same files not
recognized when put into a new directory?

Thanks,
Mike

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Re: [gmx-users] Applying a Uniform Shear

[toma0052]

Hello,
 Thanks for the rapid response, although I am not sure I completely
understand what you mean.  The accelerate option adds a constant acceleration
to whatever atoms I choose with acc_grps.  However, if I want a uniform
shear, I need to give atoms an acceleration dependent on their position
within the simulation box (z-coordinate in the case of my bilayer lying in
the x-y plane and the acceleration being in the x-direction).  I don't see
how I could do this with the accelerate mdp option.  Am I missing something
here?

Thanks,
Mike





On 13 Sep 2007, David van der Spoel wrote:
> toma0052 wrote:
> > Hello,
> >  I am looking for a way in Gromacs that I could apply a uniform
shear. 
> I
> > have looked through the manual, and it seems that the methods for
applying
> > shear are using the cos_acceleration option or the deform option.  The
> deform
> > option may work for me.  However, I was reading in Allen and Tildesley's
> book
> > about a method for applying a uniform shear which involves a modification
> to
> > the PBC (In fact, I think it is what's depicted on the book's cover). 
> > Essentially, the simulation box is held fixed, and the boxes above move
in
> > one direction (+x) and the boxes below move in the opposite direction
(-x).
> 
> > Is there any way that I can do something like this in Gromacs?  I have
> > searched the mailing list as well, but have come up empty handed.
> >  My system is a lipid bilayer in water.  I would like to look at this
> > system's response to a shear force, but I am not interested in any
> viscosity
> > calculations, so I am not sure cos_acceleration would be helpful to me. 
If
> I
> > use deform, I am worried that at long times I will get a simulation box
> with
> > some very sharp angles.  If the above procedure is not possible in
Gromacs,
> > would it make sense to use the deform option in a sinusoidal fashion
doing
> > several simulations where the box is first deformed one way and then
> deformed
> > back again in the opposite direction?
> > 
> 
> 
> you can use normal accelerations (see mdp options)
> 
> > Thank you,
> > Mike
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
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> 
> 
> -- 
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> [EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] Applying a Uniform Shear

[toma0052]

Hello,
 I am looking for a way in Gromacs that I could apply a uniform shear.  I
have looked through the manual, and it seems that the methods for applying
shear are using the cos_acceleration option or the deform option.  The deform
option may work for me.  However, I was reading in Allen and Tildesley's book
about a method for applying a uniform shear which involves a modification to
the PBC (In fact, I think it is what's depicted on the book's cover). 
Essentially, the simulation box is held fixed, and the boxes above move in
one direction (+x) and the boxes below move in the opposite direction (-x). 
Is there any way that I can do something like this in Gromacs?  I have
searched the mailing list as well, but have come up empty handed.
 My system is a lipid bilayer in water.  I would like to look at this
system's response to a shear force, but I am not interested in any viscosity
calculations, so I am not sure cos_acceleration would be helpful to me.  If I
use deform, I am worried that at long times I will get a simulation box with
some very sharp angles.  If the above procedure is not possible in Gromacs,
would it make sense to use the deform option in a sinusoidal fashion doing
several simulations where the box is first deformed one way and then deformed
back again in the opposite direction?

Thank you,
Mike

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[gmx-users] Pressure coupling and tau_p values

[toma0052]

Hello,
 I am simulating a lipid bilayer system under a shear stress, in which I
am interested in looking at the surface tension.  I have done a number of
simulations in an NPT ensemble using semiisotropic Berendsen pressure
coupling.  For a system such as this, I am wondering what would be an optimal
tau_p because I seem to be getting slightly different results dependent on
the value I choose.  For example, a 3ns simulation using a tau_p of 0.5 I get
a surface tension of 30 dynes/cm and using a tau_p of 5.0 I get a surface
tension of 25 dynes/cm.  Is this difference negligible?
 I have looked into this a bit, and I have seen a number of publications
in which people have used Berendsen pressure coupling in a lipid bilayer
system with a coupling constant of 0.5 or 1.0ps.  However, in the mailing
list, there are some posts in which it is recommended that one use a tau_p of
5.0ps to 10.0ps due to semiisotropic coupling not having the averaging effect
of isotropic coupling and using a small coupling time can add excessive noise
to the system.  Therefore, is it more reliable when simulating a lipid
bilayer system to use a short tau_p ~0.5ps or a longer tau_p ~ 5.0ps? 

Thank you,
Mike Tomasini

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[gmx-users] g_msd and make_ndx

[toma0052]

Hello,
 I am looking to measure the diffusion coefficient of a subset of water
molecules moving through a pore in a lipid bilayer.  In looking at g_msd and
the -mol option, the manual states that my index file needs references to
molecule numbers rather than atom numbers.  I was wondering how I go about
this.  The help for make_ndx is a bit unclear to me.  It seems the selections
that I make all end up giving a reference to the atom number.  Am I missing
something here?  How do I get an index file with a reference to the molecule
number?

Thanks,
Mike Tomasini  

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Re: [gmx-users] Location of files under Cygwin

[toma0052]

On 18 Apr 2007, Mark Abraham wrote:
> toma0052 wrote:
> > Hello,
> >  I am looking to edit a little bit of the source code in Gromacs, and
I
> > am having a little bit of a problem.  Normally, I am using Gromacs that
is
> > installed on a network, but I cannot edit this, so I also have Gromacs
> > installed on a personal windows machine running Cygwin.  The installation
> > seemed to work fine, as I have run many md simulations, but my question
is
> > where are the mdlib files located?  On the network Gromacs, the files are
> > located in /usr/src/GROMACS/GCC/src/mdlib.  But, under Cygwin, the folder
> > /usr/src is empty.  Am I missing something?  Are the files located in
> another
> > location?  Did I need to include specific flags during the installation
in
> > order to have the source files in src/mdlib?  Sorry if this is a silly
> > question, but in searching the computer for update.c, I am coming up
empty.
> 
> Source files aren't installed anywhere by default, they get left where 
> they are. Thus it seems your installation directory was cleaned away, if 
> your search was complete.

Thank you for the response.  That seems to be the case.  If I were to
re-install Gromacs again, what should I do so that the installation directory
and hence source files are not cleaned away?  Last time I followed the
instructions from the post: [gmx-users] HOWTO for installing non-MPI
gromacs-3.3.1 on cygwin.
What additional would I need to do to keep the source files?

Thank you,
Mike

> 
> Mark
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[gmx-users] Location of files under Cygwin

[toma0052]

Hello,
 I am looking to edit a little bit of the source code in Gromacs, and I
am having a little bit of a problem.  Normally, I am using Gromacs that is
installed on a network, but I cannot edit this, so I also have Gromacs
installed on a personal windows machine running Cygwin.  The installation
seemed to work fine, as I have run many md simulations, but my question is
where are the mdlib files located?  On the network Gromacs, the files are
located in /usr/src/GROMACS/GCC/src/mdlib.  But, under Cygwin, the folder
/usr/src is empty.  Am I missing something?  Are the files located in another
location?  Did I need to include specific flags during the installation in
order to have the source files in src/mdlib?  Sorry if this is a silly
question, but in searching the computer for update.c, I am coming up empty.

Thank you,
Mike Tomasini


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[gmx-users] Changing cos_acceleration

[toma0052]

Hello,
 I am working with a DPPC lipid bilayer system in water, and I would like
to add a shear force to the bilayer.  Preferably, this force would be a
function of the z coordinate and be maximal at the bilayer surface and decay
to zero at the box top and bottom.  For this, I have been looking a the
cos_acceleration option, but it doesn't quite give me what I want.  The
Manual says that the magnitude of the acceleration is calculated by
cos(2*pi*z/boxheight).  For the size of the bilayer and box in my system,
things happen to work out nicely if the magnutude of the acceleration were
calculated as cos(2*pi*z/boxheight - pi/2).  This would give me an
acceleration of zero at the box top and bottom as well as the center, and
maximal acceleration at roughly the bilayer top and bottom surface.  I was
wondering if there was an easy to make this switch in Gromacs?
 If there is no easy to do this, I am assuming that I have to modify the
source code.  I found in update.c a line that reads:

cosz = cos(fac*x[n][ZZ])

Would this essentially be the part I am looking for, and I would just have to
change it to: cosz = cos(fac*x[n][ZZ] - PI/2)?
Are there other parts of the source code that I would have to change besides
update.c?

Thank you,
Mike Tomasini

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Re: [gmx-users] Deshuffling a .gro file

[toma0052]

Hi,
 Thanks for the response.  Sorry that the statement of my problem was so
cumbersome.  My problem was with the noncontinuous numbering of molecules
following deshuffling using editconf.  What I am doing, is following an md
run, performing a simple transformation of the coordinates in the resulting
*.gro file (to simulate a stretch, and then relaxation of a lipid bilayer). 
The noncontinuous numbering of the molecules following deshuffling makes this
transformation much harder.  Therefore, I was hoping to get a *.gro file
which has the correct numbering following deshuffling.  However, it appears
that deshuffling and sorting the atoms in a *.gro file is quite nontrivial,
so now I have taken to not running my simulation in parallel, or not using
the -shuffle -sort option and just dealing with the longer run times.  Thanks
for the advice.

Mike



On 27 Mar 2007, Yang Ye wrote:
> On 3/20/2007 10:03 PM, toma0052 wrote:
> > Hello,
> >  I am performing a simulation in parallel on four processors.  The
> > simulation seems to run fine, and outputs a shuffled *.gro file.  I would
> > like to change the order of atoms to what they were in the original input
> > *.gro file, but I am having some trouble.  I have seen some previous
posts
> > on this, but I am still a bit confused. 
> >
> > David van der Spoel wrote:
> >   
> > [...]
> >
> >   
> >> If your standard dsehuf.ndx for a system of N atoms starts with:
> >> [ deshuf ]
> >> 0 1 4 6 7 etc.
> >> you have to modify it to the old format:
> >> 1 N
> >> deshuf N
> >> 0 1 4 6 7 etc.
> >>
> >> You only have to change the top bit, not the actual numbers. An
> >> alternative is to modify it to be:
> >> [ deshuf ]
> >> 1 2 5 7 8 etc.
> >>
> >> That wouldn't be too hard with a script either.
> >>
> >> 
> >
> > This says that I need to alter my deshuf.ndx file a bit, and then just do
> > editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  to obtain an unchuffled
> > *.gro file.  However, my deshuf.ndx file already began counting the atoms
> > at 1, i.e.:
> >
> > [ DeShuffle ]
> >   1  2  3  4  5  6  7  8  9  10
> >   11  12  13  14  15  16  17  18  19  20
> >   21  22  23  24  25  26  27  28  29  30
> >   31  32  33  34  35  36  37  38  39  40
> >   41  42  43  44  45  46  47  48  49  50
> > ...
> >
> > So, everything already seems to be fine (other than the name in the
> > brackets, which didn't seem to matter if changed) with the deshuf.ndx
file.
> >  When I do editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  though, my
> > *.gro file does not sort properly, although some sorting does take place.

> > The atoms seem to be in the correct general order (The first series of
> > atoms are all DPPC, and the rest are all SOL) but the atom numbers are in
> > the wrong order (The order goes 1DPPC ... 44DPPC, 1257DPPC ... 1299DPPC,
> > 2513DPPC ... etc whereas it should go from 1DPPC to 128DPPC and then
begin
> > to number the SOL molecules at 129SOL).  Is this a problem with my input
> > into grompp?  I am using both -shuffle and -sort.  Is this incorrect?
> > How do I deshuffle my *.gro file to list the 128 DPPC molecules and then
> > the 3655 SOL molecules with atom numbers 1 to 17365?
> >   
> Sorry that your description was not easy to be comprehend. Perhaps this 
> is why this post was not followed.
> I would like to offer some general principles here.
> 1. deshuf.ndx is definitely not ordered so you shall see some 
> disordering in the later part of ndx file.
> 2. After deshuffling using editconf, it is normal for the resulting .gro 
> to have noncontinuous numbering for molecule. It is more important to 
> have the correct molecule type. For example, all your SOL shall be in 
> one block with no other molecules embedded.
> 
> 
> Yang Ye
> > Thank you,
> > Mike Tomasini
> >
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> >   
> 
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Re: [gmx-users] grompp error with cpp

[toma0052]

Thanks for the reply,
 I have tried changing the mdp file so it looks for the cpp in /lib/cpp,
/lib/cpp.exe, /bin/cpp, and /bin/cpp.exe and all of these produce the same
message as below, that the cpp file does not exist.  It had worked when I ran
a simulation before with the mdp file as /lib/cpp, but I am not sure why it
is not working now.  Should I just try to reinstall Gromacs?

Thanks,
Mike


On 24 Mar 2007, David van der Spoel wrote:
> toma0052 wrote:
> > Hello,
> >  I just installed Gromacs on my windows machine under cygwin, and
> > everything seemed to go fine with the installation and whatnot. 
Initially,
> > when I tried to run a simulation, I obtained the error that Gromacs found
> the
> > number of coordinates in my .top file to be 0, because it could not find
> the
> > cpp.  From the mailing list archives, I gathered that Gromacs was
checking
> > for cpp in /lib/cpp whereas in cygwin the cpp is in /bin/cpp.  So, as in
> the
> > post, I created a link in /lib pointing to /bin/cpp.  I ran a simulation,
> and
> > everything went fine.  Now, I am trying to run another simulation, and I
am
> > running into the same problem as before.  When I execute grompp, I get
this
> > error:
> >  
> > Back Off! I just backed up md_shear_run.mdp to ./#md_shear_run.mdp.2#
> > checking input for internal consistency...
> > ...ling /lib/cpp
> > : No such file or directory
> > cpp exit code: 32512
> 
> replace /lib/cpp with /bin/cpp (with or without .exe) in the mdp file
> 
> 
> 
> -- 
> 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] grompp error with cpp

[toma0052]

Hello,
 I just installed Gromacs on my windows machine under cygwin, and
everything seemed to go fine with the installation and whatnot.  Initially,
when I tried to run a simulation, I obtained the error that Gromacs found the
number of coordinates in my .top file to be 0, because it could not find the
cpp.  From the mailing list archives, I gathered that Gromacs was checking
for cpp in /lib/cpp whereas in cygwin the cpp is in /bin/cpp.  So, as in the
post, I created a link in /lib pointing to /bin/cpp.  I ran a simulation, and
everything went fine.  Now, I am trying to run another simulation, and I am
running into the same problem as before.  When I execute grompp, I get this
error:
 
Back Off! I just backed up md_shear_run.mdp to ./#md_shear_run.mdp.2#
checking input for internal consistency...
...ling /lib/cpp
: No such file or directory
cpp exit code: 32512
 dppc.top > gromppt9guCt're/gromacs/top -DPOSRES
' command is defined in the .mdp file
processing topology...
processing coordinates...
---
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (md_start_1000.gro, 17365)
 does not match topology (dppc.top, 0)
---

>From this, I gather that Gromacs cannot find the cpp, however, if I look in
/lib, the file cpp.exe exists there.  I don't think that I have changed
anything with the paths since my last successful run, so why now can Gromacs
not locate the cpp?  Is there something that I am missing?

Thanks,
Mike Tomasini

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[gmx-users] Deshuffling a .gro file

[toma0052]

Hello,
 I am performing a simulation in parallel on four processors.  The
simulation seems to run fine, and outputs a shuffled *.gro file.  I would
like to change the order of atoms to what they were in the original input
*.gro file, but I am having some trouble.  I have seen some previous posts
on this, but I am still a bit confused. 

David van der Spoel wrote:
> 
[...]

> If your standard dsehuf.ndx for a system of N atoms starts with:
> [ deshuf ]
> 0 1 4 6 7 etc.
> you have to modify it to the old format:
> 1 N
> deshuf N
> 0 1 4 6 7 etc.
> 
> You only have to change the top bit, not the actual numbers. An
> alternative is to modify it to be:
> [ deshuf ]
> 1 2 5 7 8 etc.
> 
> That wouldn't be too hard with a script either.
> 

This says that I need to alter my deshuf.ndx file a bit, and then just do
editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  to obtain an unchuffled
*.gro file.  However, my deshuf.ndx file already began counting the atoms
at 1, i.e.:

[ DeShuffle ]
  1  2  3  4  5  6  7  8  9  10
  11  12  13  14  15  16  17  18  19  20
  21  22  23  24  25  26  27  28  29  30
  31  32  33  34  35  36  37  38  39  40
  41  42  43  44  45  46  47  48  49  50
...

So, everything already seems to be fine (other than the name in the
brackets, which didn't seem to matter if changed) with the deshuf.ndx file.
 When I do editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  though, my
*.gro file does not sort properly, although some sorting does take place. 
The atoms seem to be in the correct general order (The first series of
atoms are all DPPC, and the rest are all SOL) but the atom numbers are in
the wrong order (The order goes 1DPPC ... 44DPPC, 1257DPPC ... 1299DPPC,
2513DPPC ... etc whereas it should go from 1DPPC to 128DPPC and then begin
to number the SOL molecules at 129SOL).  Is this a problem with my input
into grompp?  I am using both -shuffle and -sort.  Is this incorrect?
How do I deshuffle my *.gro file to list the 128 DPPC molecules and then
the 3655 SOL molecules with atom numbers 1 to 17365?

Thank you,
Mike Tomasini

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Re: [gmx-users] Frozen atoms and energy group exclusion

[toma0052]

Hello,
 Thanks for the fast response.  I went through my dppc.itp file and chose
atoms such that the group of frozen atoms has a net charge of 0 as does the
rest of the molecule.  When running this through grompp, the error before
about the atoms being in different charge groups is gone.  However, the
warning (WARNING 1 [file "dppc.top", line 19]: Can not exclude the lattice
Coulomb energy between energy groups) is still present.  What exactly does
this warning mean?  Will this have a large affect on my simulation output?

Mike Tomasini




On 5 Mar 2007, Mark Abraham wrote:
> >  When I run this through grompp, I get the following error:
> > WARNING 1 [file "dppc.top", line 19]:
> >   Can not exclude the lattice Coulomb energy between energy groups
> > Checking consistency between energy and charge groups...
> > ---
> > Program grompp, VERSION 3.3
> > Source code file: grompp.c, line: 307
> >
> > Fatal error:
> > atoms 3212 and 3213 in charge group 2179 are in different energy groups
> > ---
> >
> > Am I doing this incorrectly?  Should I be excluding the interactions wi=
> th
> > the
> > frozen groups in another way?
> 
> Have a look at the description of charge groups in 4.6.2 and 4.6.3 and th=
> e
> implementation of this in 5.5.1. grompp is evidently complaining that you=
> r
> charge group boundaries are not the same as the energy group boundaries,
> and since non-bonded energies are calculated looping over charge groups,
> this is a fine thing for it to be unhappy about! So have a look at the
> charge groups in your DPPC molecule and see if you can come up with a
> compromise that keeps charge group neutrality.
> 
> Mark
> 
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[gmx-users] Frozen atoms and energy group exclusion

[toma0052]

Hello,
 I asked a similar question to this a bit ago, but didn't get much of a
response.  I have a lipid bilayer system of 128 DPPC molecules in water.  I
want to fix the bottom face of the bilayer, and I am doing so by freezing the
positions of the first 12 atoms of the DPPC molecule.  The manual says that
with frozen groups, one should use energy group exclusions to avoid odd force
contributions. So, in my .mdp file, I define one energy group as froz (The
first 12 atoms of the DPPC molecules on the bottom face), and another as
not_excl (Everything that is not froz).  Then, I use:  energygrp_excl   =  
froz froz froz not_excl
to exclude the interaction of the frozen atoms with themselves and the
interaction between the frozen atoms and the rest of the system.
 When I run this through grompp, I get the following error:
WARNING 1 [file "dppc.top", line 19]:
  Can not exclude the lattice Coulomb energy between energy groups
Checking consistency between energy and charge groups...
---
Program grompp, VERSION 3.3
Source code file: grompp.c, line: 307

Fatal error:
atoms 3212 and 3213 in charge group 2179 are in different energy groups
---

Am I doing this incorrectly?  Should I be excluding the interactions with the
frozen groups in another way?  My dppc.top file, of which line 19 is the end,
looks as follows:

; topology for a pure DPPC bilayer with 128 lipids and 3655 SPC water
; molecules
#include "ffgmx.itp"
#include "dppc.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
Pure DPPC bilayer with 128 lipids and 3655 water molecules

[ molecules ]
; name  number
DPPC128
SOL 3655SOL

Thank you,
Mike Tomasini


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[gmx-users] Simulation in parts

[toma0052]

Hello,
 I was wondering if I could run a simulation in parts.  I would like to
run a simulation for 100ps say, analyze it, and then sometime later continue
on for another 100ps.  It seems like all I would need to do is take the
*.gro, *.trr, and *.edr files output from the first md simulation, feed it
back in to grompp and use mdrun.  I have tried this, and the output from the
run seems okay, but I am not completely sure.  The output of grompp says; 
Velocities generated: ignoring velocities from input trajectory.  Will this
cause a disjoint between the two simulations?  Is there a way that I can have
the velocities from the end of the first md simulation, input into the
second?  Also, I used -time 100 and grompp says;  Reading frame500 time 
100.000   Using frame at t = 100 ps 
Starting time for run is 0 ps
Is there a way that I can have the starting time for the second run be 100ps
so that the numbers match up in the *.edr files and the second run goes from
100ps to 200ps?

Thanks,
Mike Tomasini

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[gmx-users] Constant normal pressure simulation

[toma0052]

Hello,
 I am looking to do a membrane simulation where I have a constant
pressure normal to the membrane, and a fixed area of the membrane.  Being
semi-unfamiliar with pressure coupling schemes, how would I do this in
Gromacs?  It seems that even if I use the semiisotropic pressure coupling
scheme, the simulation box will rescale to maintain whatever pressure I name
for the x and y directions.  I want the x and y box dimensions to stay fixed
with only the z box dimension allowed to fluctuate, as done by
Sankararamakrishnan and Weinstein, 2004.

Thank you,
Mike

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[gmx-users] Pressure coupling question

[toma0052]

Hello,
 I am simulating a lipid bilayer system, and am having some trouble
understanding the pressure output.  When I run a simulation, even when I do
not add any perturbations or fix any atoms, the pressure oscillations are
quite large.  The temperature coupling seems fine.  After about 1ps, the
system is near the reference temperature, and the oscillations are only about
1 or 2 degrees.  So, I expected something, roughly, similar with the
pressure.  For the pressure, however, my reference pressure is 1.0 bar, but
the pressure in the system after a few picoseconds seems to range from -400
to 400 bar.  Is this normal?  Do I just need to wait longer?  Does this mean
that I did not run the energy minimization long enough and there are some
high forces?  Is there something else that I am doing wrong?
 In my mdp file, the pressure coupling looks like:
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p= 0.5
compressibility  = 4e-5
ref_p= 1.0

I have also tried Parrinello-Rahman pressure coupling with the same result.

Thanks
Mike

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[gmx-users] Help with energygrp_excl

[toma0052]

Hello,
 I am doing some simulations on a DPPC bilayer that I got from Dr.
Tieleman's website.  I would like to examine shear forces necessary for
membrane rupture.  To do this, I have applied an acceleration to the head
(First 12 atoms of each DPPC molecule, as numbered in the topology file) of
the upper leaflet while keeping the positions of the same 12 atoms of the
bottom leaflet restrained.  The rest of the atoms of the DPPC molecules are
free to go where the forces take them.
 After the md run, the numbers that I get for the pressure and the
surface tension of the system are much larger than I would expect them to be.
 I am assuming that this is because of the restrained atoms, so I would like
to add to my .mdp file energy group exclusions.  However, if I define my
energy groups as:

energygrp  = DPPC SOL acc res
energygrp_excl = res res  res DPPC  res SOL  res acc

I get the error that some atoms belong to more than one energy group when
putting everything through grompp.
 So, when I make another group that is all atoms not res (the restrained
atoms, I called energy1) and do:

energygrp  = res energy1
energygrp_excl = res res  res energy1

I get a different error that says "atoms 3212 and 3213 in charge group 2179
are in different energy groups".  However, this seems to be what I want,
since atom 3213 is in the group that is restrained whereas atom 3212 is not.
 Am I setting up energy group exclusions incorrectly?  How do I exclude
the contributions from the restrained atoms in my pressure and surface
tension calculations?

Thank you,
Mike Tomasini

Here is my mdp file if that in any way helps:

title= DPPC shear simulation
;Preprocessor
cpp  = /lib/cpp
:Directories to include in the topology format
include  = -I.../top
;Include definition for position restraints
define   = -DPOSRES
integrator   = md
;Simulation time of 100 ps
dt   = 0.002; In picoseconds
nsteps   = 5
;
nstxout  = 100
nstvout  = 100
nstfout  = 1000 
nstlog   = 10
nstenergy= 10
;
nstlist  = 5
ns_type  = grid
;
rlist= 0.9
coulombtype  = PME
rcoulomb = 0.9
rvdw = 1.4
fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 4
ewald_rtol   = 1e-5
optimize_fft = yes
;
pbc  = xyz
;Temperature Coupling
tcoupl   = berendsen
tc-grps  = DPPC SOL   
tau_t= 0.1 0.1  
ref_t= 310 310
;Pressure Coupling
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
;Velocity generation
gen_vel  = yes 
gen_temp = 310
gen_seed = 133529
;Constraints?
;
;Energy group exclusion for position restraints
energygrps   = res energy1
energygrp_excl   = res res  res energy1  ;Correct?
;energygrps  = res acc DPPC SOL
;energygrp_excl  = res res  res acc  res DPPC  res SOL
;
;Accelerate top layer
acc_grps = acc
accelerate   = 1.0 0.0 0.0
;Freeze bottom layer
freezegrps   = res
freezedim= Y Y Y


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[gmx-users] Surface Tension of a lipid bilayer

[toma0052]

Hello,
 I have a question about calculating the surface tension for the
water-lipid interface of a lipid bilayer.  After an MD run, I can use my .edr
file and g_energy to calculate the surface tension.  I believe that the
surface tension is calculated something like gamma = (Pzz-(Pxx+Pyy)/2)/L.  I
was wondering though, is the pressure tensor and hence surface tension
calculated over the entire simulation box?  I would assume so, since I did
not specify any molecules.  To find the water-lipid surface tension, would I
not need to sum over only the molecules at the surface?  Would this be
do-able in Gromacs?  Would I have to write something separate to do this?
 In my coordinate file, I have DPPC atoms, solvent atoms, and other atoms
(those that make up the head group ie O,N etc.).  Could I just make an index
group that is not DPPC and not Solvent, and sum over those atoms?

Thanks,
Mike Tomasini

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Re: [gmx-users] indexing atoms *Altering code

[toma0052]

Hi,
 Thank you for the response.  Being that Fortran is much more my
language of choice than C, I was wondering if someone could point me in the
right direction as far as modifying the C code to do what I want.  It is my
understanding that an mdrun begins by making a neighbor list, computing the
forces, globally summing the forces, and then updating the positions and
velocities.  So I am assuming that, just after globally summing the forces,
I can run an if statement  over all of the solvent molecules testing
whether their z-coordinate is within certain bounds, and if so, simply add
Fsum = Fsum + Fext.  My question is, where do I do this?  Do I have to do
it in multiple files?  Where are those files stored in Gromacs?  Is it the
mdrun.h and force.h files that I need to modify?  Sorry if this should be
obvious, but again, my C skills are not the best.

Thank you,
Mike  



On 29 Nov 2006, Mark Abraham wrote:
> toma0052 wrote:
> > Hello,
> >  I am wondering about a response I got a while ago about indexing
> > atoms.  I am not very familiar with awk, but it seems like a fairly
simple
> > way to search through a .gro file and find the solvent molecules with a
> > particular z-coordinate range, as I need for my simulation.  My
question
> > however, concerns  implementing this into an md run.  I would like to
add
> > an acceleration to solvent molecules that are within a certain distance
> > from a lipid bilayer.  However, if the solvent molecules diffuse too
far
> > away during the md run, I no longer want them to have an acceleration. 
> > Therefore, it appears that at every time step I need to perform a check
to
> > see which solvent molecules are close enough to warrant an
acceleration. 
> > So, is there a way that I can incorporate the awk file such that it
runs
> > and creates a particular index group at every time step?  If not, is
there
> > some other way that I can check at each time step (or every several
time
> > steps) which solvent molecules have a particular z-coordinate and give
them
> > an acceleration?
> 
> I presume you've read the relevant manual sections. If there's nothing 
> useful there, the only way to do something like this would be to get 
> inside the C code, loop over all solvent molecules after do_force to 
> check for their position, and then adjust the force on them accordingly.
> 
> Mark
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Re: [gmx-users] indexing atoms

[toma0052]

Hello,
 I am wondering about a response I got a while ago about indexing
atoms.  I am not very familiar with awk, but it seems like a fairly simple
way to search through a .gro file and find the solvent molecules with a
particular z-coordinate range, as I need for my simulation.  My question
however, concerns  implementing this into an md run.  I would like to add
an acceleration to solvent molecules that are within a certain distance
from a lipid bilayer.  However, if the solvent molecules diffuse too far
away during the md run, I no longer want them to have an acceleration. 
Therefore, it appears that at every time step I need to perform a check to
see which solvent molecules are close enough to warrant an acceleration. 
So, is there a way that I can incorporate the awk file such that it runs
and creates a particular index group at every time step?  If not, is there
some other way that I can check at each time step (or every several time
steps) which solvent molecules have a particular z-coordinate and give them
an acceleration?

Thank you,
Mike Tomasini






On 31 Oct 2006, Erik Marklund wrote:
> You can sort the atoms according to position using grompp, but I don't
> think that's the easiest solution. I would use awk or something along
> those lines, to find all atoms within z=3D[4 5] nm and remove everything
> except the indexes. Put a bracketed name on top of it all and
viol=C3=A0,=
>  you
> have turned them into an index group.
> 
> /Erik
> 
> On Tue, 2006-10-31 at 00:37 -0600, toma0052 wrote:
> > Hello,
> >  I have a question regarding indexing atoms for use with
> > non-equilibrium MD.  The manual says that I can select atoms by number
=
> or
> > type; I was wondering if there is a way in Gromacs to index atoms by
> > position with the simulation box.  I am looking to add an acceleration
=
> to
> > the solvent, but not the entire solvent.  Is there a way that I can
spe=
> cify
> > solvent molecules within a certain coordinate ie. a z-position from
4nm=
>  to
> > 5nm with the simulation box being 6nm in height?  I am looking to
> > accelerate solvent molecules near a lipid bilayer, but if a particular
> > solvent molecule diffuses too far from the bilayer, I no longer want
it=
>  to
> > keep its fixed acceleration.  Is there any way that indexing by
coordin=
> ates
> > is possible?
> >=20
> > Thank you,
> > Mike Tomasini
> >=20
> > ___
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> --=20
> Erik Marklund, PhD Student, Molecular Biopcysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone: +46 18 471 4537  fax: +46 18 511 755
> [EMAIL PROTECTED]
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[gmx-users] indexing atoms

[toma0052]

Hello,
 I have a question regarding indexing atoms for use with
non-equilibrium MD.  The manual says that I can select atoms by number or
type; I was wondering if there is a way in Gromacs to index atoms by
position with the simulation box.  I am looking to add an acceleration to
the solvent, but not the entire solvent.  Is there a way that I can specify
solvent molecules within a certain coordinate ie. a z-position from 4nm to
5nm with the simulation box being 6nm in height?  I am looking to
accelerate solvent molecules near a lipid bilayer, but if a particular
solvent molecule diffuses too far from the bilayer, I no longer want it to
keep its fixed acceleration.  Is there any way that indexing by coordinates
is possible?

Thank you,
Mike Tomasini

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Re: [gmx-users] 1-4 Interactions

[toma0052]

Hi,
 Thanks for the prompt responses.  I checked the distance between atoms
908 and 913 in VMD and got 0.396nm, which seems fine.  I thought then, that
my problem may be with my box size when I used editconf.  When I changed
the box dimension to 2.0nm from the molecule periphery, the warning between
atoms 908 and 913 disappeared.  However, I then recieved a similar error 

warning: interaction between 911 and 932 at distance 6.244 which is larger
than the 1-4 table size 1.000 nm

I checked atoms 911 and 932 using VMD, and they don't appear to be close at
all, and their distance is in fact 6.244nm.  Does this mean that there is a
problem with my topology file?  My topology file is the same as that given
on Tieleman's site, except that I removed #include "lipid.itp".  This was
giving me an error, and I did download the ffgmx_lipids.tar.gz file from
the Gromacs site, which seemed to solve the problem.  So, I am not sure why
this error is occuring.  The problem could be with my em.mdp file.  I am
new to Gromacs, and so I used the em.mdp file from John Kerrigan, which is
below.  If anyone has any ideas, that would be great.

Thanks,
Mike Tomasini

em.mdp

title   =  DPPC
cpp =  /lib/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  steep
dt  =  0.002; ps
nsteps  =  400
nstlist =  5
ns_type =  grid
pbc =  full
rlist   =  0.9
table-extension =  1
coulombtype =  PME
rcoulomb=  0.9
rvdw=  1.4
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft  =  yes
;
;   Energy minimizing stuff
;
emtol   =  1000
emstep  =  0.01






On 19 Oct 2006, Tsjerk Wassenaar wrote:
> Hi Mike,
> 
> A 1-4 interaction is an interaction between two atoms which are
> attached to each other with three bonds in between (two other atoms,
> 1-2-3-4). Based on the normal bond lengths, angles, etc. two such
> atoms should not be further away from each other than 1 nm. Check the
> atom locations of 908 and 913 in a viewer and try to see what is wrong
> (also check the topology and the box).
> 
> Best,
> 
> Tsjerk
> 
> On 10/19/06, Mark Abraham <[EMAIL PROTECTED]> wrote:
> > toma0052 wrote:
> > > Hello,
> > >  I am starting simulations on a DPPC lipid bilayer taken from
Peter
> > > Tieleman's website.  Upon trying to run the energy minimization, the
> > > program runs, but the results does not appear correct.  During the
run, I
> > > get the warning:
> > >
> > > Warning: 1-4 interaction between 908 and 913 at distance 1.621 which
is
> > > larger than the 1-4 table size 1.000 nm.  These are ignored for the
rest
> of
> > > the simulation.  This usually means your system is exploding, if not,
you
> > > should increase table-extension in your mdp file.
> > >
> > > I have tried increasing the table-extension in my em.mdp file, but I
need
> > > to increase it to over 10nm in order for that error to go away. 
Could
> > > someone explain a little bit more on what the table-extension and 1-4
> > > interactions are, and what could possibly be wrong with my energy
> > > minimization.  All I have done so far is to take the dppc128.pdb file
and
> > > the example2.top topology file from Peter Tieleman's site, run
editconf
> and
> > > grompp with en em.mdp file similar to John Kerrigan's tutorial,
followed
> by
> > > mdrun.  Any help would be appreciated.
> >
> > My guess is the topology is broken, or doesn't correspond to the
> > configuration. Get out VMD or something and look at things visually.
> >
> > Mark
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> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
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[gmx-users] 1-4 Interactions

[toma0052]

Hello,
 I am starting simulations on a DPPC lipid bilayer taken from Peter
Tieleman's website.  Upon trying to run the energy minimization, the
program runs, but the results does not appear correct.  During the run, I
get the warning:

Warning: 1-4 interaction between 908 and 913 at distance 1.621 which is
larger than the 1-4 table size 1.000 nm.  These are ignored for the rest of
the simulation.  This usually means your system is exploding, if not, you
should increase table-extension in your mdp file.

I have tried increasing the table-extension in my em.mdp file, but I need
to increase it to over 10nm in order for that error to go away.  Could
someone explain a little bit more on what the table-extension and 1-4
interactions are, and what could possibly be wrong with my energy
minimization.  All I have done so far is to take the dppc128.pdb file and
the example2.top topology file from Peter Tieleman's site, run editconf and
grompp with en em.mdp file similar to John Kerrigan's tutorial, followed by
mdrun.  Any help would be appreciated.

Thanks,
Mike Tomasini


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[gmx-users] p_4 error

[toma0052]

Hello,
 I am running a simulation and when I attempt to use mdrun, I get the
error p_4 error: interrupt SIGSEGV:11.  I am not sure what this error is,
but p_4 error apparently has something to do with shared programs.  Also,
strangly enough, when I type mdrun -h, I get the help information, but at
the end of the file I get:

[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_25033: p4_ error: : 0

Another p_4 error.  Does this mean that the MPICH is somewhere set up
incorrectly for dealing with Gromacs?  Should I reinstall Gromacs?  Is
there something else that I should be doing?

Thanks,
Mike Tomasini


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[gmx-users] External Forces

[toma0052]

Hello,
 I am simulating a DPPC lipid bi-layer, and I would like to add an
external force to, for example, one layer of the bilayer.  Do I add
an external force by specifying groups and the acceleration on those
groups in the mdp file?  Is there another way to do this?  Do I need
to alter any other files?

Thanks,
Mike




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[gmx-users] Error with mdrun

[toma0052]

Hi,
I am trying to run a lipid bilayer simulation, and everything seems to 
be fine until I try to run mdrun. The simulation stops immediately after I 
begin mdrun, and I receive the error; p4_error: interrupt SIGSEV: 11. I am 
not really sure what this error is, nor what I should do to try to fix it. 
Any help would be appreciated.


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[gmx-users] Lipid Bilayer Simulations

[toma0052]

Hi,
 I am new to Gromacs, and I am working with lipid bilayer simulations. 
I am attempting to just run an energy minimization on a lipid bilayer so I
can get a better feel for the program.  I have taken the files dppc128.pdb,
dppc.itp, lipid.itp and example2.itp from Peter Tieleman's website. 
Because I could not use teh pdb2gmx command, I started with the editconf
command and then the genbox command, both of which seemed to run
successfully.  Then, I tried to do the preprocessing with the grompp
command, but I received the error; Fatal Error: Found a second defaults
directive, file "lipid.itp".  When I removed lipid.itp from the topology
file, I received the error; Fatal Error: Atomtype 'LC3' not found!  As I
said before, I am new to Gromacs, and I am not sure how to get around this
problem. Do I need to put the dppc.itp and lipid.itp file together into
one?  Any help would be appreciated.

Thanks,
Mike Tomasini

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[gmx-users] Lipid simulations

[toma0052]

Hello,
 I am just starting MD simulations of lipid bilayers using Gromacs.  I
am looking to add a force to a cetain set of atoms, one layer of a bilayer.
 I was wondering in anyone knew what program files I would need to modify
in order to do this.

Thanks,
Mike Tomasini

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[gmx-users] Surface Tension Calculation

[toma0052]

Hi,
 I posted a question a few days ago regarding the calculation of the
surface tension of a lipid bilayer in Gromacs.  The response that I got was
to use the option "#Surf*SurfTens" in g_energy.  I am not really sure how
to do this.  I have looked at the g-energy file in Gromacs, and I don't see
any option that is "#Surf*SurfTens".  Maybe the file name is wrong, or I am
running an older version of Gromacs or something.  Let me know if is there
is a way to calculate the surface tension of a lipid bilayer within the
Gromacs program, or if it is necessary for me to modify the code.  (The
more detailed the better. I am new to Gromacs)

Thanks,
Mike Tomasini

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[gmx-users] Gromacs Surface tension

[toma0052]

Hi,
 I am not sure if this is how I should ask questions regarding Gromacs,
but here goes.  I was wondering if anyone knows if there is an internal
program in Gromacs for calculating surface tension.  I would like to model
a lipid bilayer, and then determine the surface tension on that bilayer
under certain conditions.  Is there an included way for me to do that in
Gromacs, or do I need to modify the Gromacs code?

Thanks,
Mike

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