Commit 7b7e1694 authored by eric pellegrini's avatar eric pellegrini

repopulate MDANSE

parent 5a2bf9e8
SPCE box
units kJ
molecular types 1
spce water
nummols 256
atoms 3
OW 16.0000 -0.82000 1 0 0d.a
HW 1.0000 0.41000 1 0 0.h.
HW 1.0000 0.41000 1 0 0.h.
constraints 3
1 2 1.000
1 3 1.000
2 3 1.633
finish
vdW 3
OW OW 12-6 0.26330E+07 2617.0 1.0000 1.0000 1.0000
OW HW 12-6 0.00000E+00 0.00000E+00 1.0000 1.0000 1.0000
HW HW 12-6 0.00000E+00 0.00000E+00 1.0000 1.0000 1.0000
close
Automatic FIELD created for 1 molecule of Cumene
units kJ
molecules 1
Cumene
nummols 1
atoms 21
CB 12.0110 -0.1150 1 0
CB 12.0110 -0.1150 1 0
CB 12.0110 -0.1150 1 0
CB 12.0110 -0.1150 1 0
CS 12.0110 0.0000 1 0
CB 12.0110 -0.1150 1 0
C3 12.0110 -0.0600 1 0
C1 12.0110 -0.1800 1 0
C1 12.0110 -0.1800 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HB 1.0080 0.1150 1 0
HB 1.0080 0.1150 1 0
HB 1.0080 0.1150 1 0
HB 1.0080 0.1150 1 0
HB 1.0080 0.1150 1 0
HR 1.0080 0.0600 1 0
bonds 21
harm 7 8 2594.0801 1.526
harm 7 9 2594.0801 1.526
harm 5 7 2652.6560 1.520
harm 4 5 3924.5920 1.400
harm 5 6 3924.5920 1.400
harm 1 2 3924.5920 1.400
harm 1 6 3924.5920 1.400
harm 2 3 3924.5920 1.400
harm 3 4 3924.5920 1.400
harm 1 19 3071.0559 1.080
harm 2 18 3071.0559 1.080
harm 3 17 3071.0559 1.080
harm 4 16 3071.0559 1.080
harm 6 20 3071.0559 1.080
harm 8 13 2845.1201 1.090
harm 8 14 2845.1201 1.090
harm 8 15 2845.1201 1.090
harm 9 10 2845.1201 1.090
harm 9 11 2845.1201 1.090
harm 9 12 2845.1201 1.090
harm 7 21 2845.1201 1.090
angles 36
harm 1 2 3 527.1840 120.000
harm 2 1 6 527.1840 120.000
harm 2 3 4 527.1840 120.000
harm 1 6 5 527.1840 120.000
harm 3 4 5 527.1840 120.000
harm 4 5 6 527.1840 120.000
harm 4 5 7 585.7600 120.000
harm 6 5 7 585.7600 120.000
harm 1 2 18 292.8800 120.000
harm 1 6 20 292.8800 120.000
harm 2 1 19 292.8800 120.000
harm 2 3 17 292.8800 120.000
harm 3 2 18 292.8800 120.000
harm 3 4 16 292.8800 120.000
harm 4 3 17 292.8800 120.000
harm 6 1 19 292.8800 120.000
harm 5 4 16 292.8800 120.000
harm 5 6 20 292.8800 120.000
harm 5 7 8 527.1840 114.000
harm 5 7 9 527.1840 114.000
harm 8 7 9 334.7200 109.500
harm 5 7 21 418.4000 109.500
harm 8 7 21 418.4000 109.500
harm 9 7 21 418.4000 109.500
harm 7 8 13 418.4000 109.500
harm 7 8 14 418.4000 109.500
harm 7 8 15 418.4000 109.500
harm 7 9 10 418.4000 109.500
harm 7 9 11 418.4000 109.500
harm 7 9 12 418.4000 109.500
harm 10 9 11 585.7600 109.500
harm 10 9 12 585.7600 109.500
harm 11 9 12 585.7600 109.500
harm 13 8 14 585.7600 109.500
harm 13 8 15 585.7600 109.500
harm 14 8 15 585.7600 109.500
dihedrals 48
cos 1 2 3 4 60.6680 180.0000 2.0000 0.50 0.50
cos 3 2 1 6 60.6680 180.0000 2.0000 0.50 0.50
cos 1 6 5 4 60.6680 180.0000 2.0000 0.50 0.50
cos 3 4 5 6 60.6680 180.0000 2.0000 0.50 0.50
cos 2 1 6 5 60.6680 180.0000 2.0000 0.50 0.50
cos 2 3 4 5 60.6680 180.0000 2.0000 0.50 0.50
cos 1 2 3 17 60.6680 180.0000 2.0000 0.50 0.50
cos 2 1 6 20 60.6680 180.0000 2.0000 0.50 0.50
cos 2 3 4 16 60.6680 180.0000 2.0000 0.50 0.50
cos 3 2 1 19 60.6680 180.0000 2.0000 0.50 0.50
cos 4 3 2 18 60.6680 180.0000 2.0000 0.50 0.50
cos 6 1 2 18 60.6680 180.0000 2.0000 0.50 0.50
cos 5 4 3 17 60.6680 180.0000 2.0000 0.50 0.50
cos 5 6 1 19 60.6680 180.0000 2.0000 0.50 0.50
cos 4 5 6 20 60.6680 180.0000 2.0000 0.50 0.50
cos 6 5 4 16 60.6680 180.0000 2.0000 0.50 0.50
cos 16 4 3 17 60.6680 180.0000 2.0000 0.50 0.50
cos 17 3 2 18 60.6680 180.0000 2.0000 0.50 0.50
cos 18 2 1 19 60.6680 180.0000 2.0000 0.50 0.50
cos 19 1 6 20 60.6680 180.0000 2.0000 0.50 0.50
cos 1 6 5 7 60.6680 180.0000 2.0000 0.50 0.50
cos 3 4 5 7 60.6680 180.0000 2.0000 0.50 0.50
cos 7 5 4 16 60.6680 180.0000 2.0000 0.50 0.50
cos 7 5 6 20 60.6680 180.0000 2.0000 0.50 0.50
cos 4 5 7 8 0.0000 0.0000 2.0000 0.50 0.50
cos 4 5 7 9 0.0000 0.0000 2.0000 0.50 0.50
cos 6 5 7 8 0.0000 0.0000 2.0000 0.50 0.50
cos 6 5 7 9 0.0000 0.0000 2.0000 0.50 0.50
cos 4 5 7 21 0.0000 0.0000 2.0000 0.50 0.50
cos 6 5 7 21 0.0000 0.0000 2.0000 0.50 0.50
cos 5 7 8 13 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 8 14 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 8 15 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 9 10 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 9 11 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 9 12 5.8576 0.0000 3.0000 0.50 0.50
cos 10 9 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 11 9 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 12 9 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 13 8 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 14 8 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 15 8 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 8 7 9 10 5.8576 0.0000 3.0000 0.50 0.50
cos 8 7 9 11 5.8576 0.0000 3.0000 0.50 0.50
cos 8 7 9 12 5.8576 0.0000 3.0000 0.50 0.50
cos 9 7 8 13 5.8576 0.0000 3.0000 0.50 0.50
cos 9 7 8 14 5.8576 0.0000 3.0000 0.50 0.50
cos 9 7 8 15 5.8576 0.0000 3.0000 0.50 0.50
finish
vdw 21
HB HB lj 0.125520 2.420000
HB HR lj 0.125520 2.460000
HB CB lj 0.191735 2.985000
HB C3 lj 0.186176 2.960000
HB C1 lj 0.186176 2.960000
HB CS lj 0.191735 2.985000
HR HR lj 0.125520 2.500000
HR CB lj 0.191735 3.025000
HR C3 lj 0.186176 3.000000
HR C1 lj 0.186176 3.000000
HR CS lj 0.191735 3.025000
CB CB lj 0.292880 3.550000
CB C3 lj 0.284389 3.525000
CB C1 lj 0.284389 3.525000
CB CS lj 0.292880 3.550000
C3 C3 lj 0.276144 3.500000
C3 C1 lj 0.276144 3.500000
C3 CS lj 0.284389 3.525000
C1 C1 lj 0.276144 3.500000
C1 CS lj 0.284389 3.525000
CS CS lj 0.292880 3.550000
close
This diff is collapsed.
methanol
units kJ
molecules 1
methanol
nummols 1000
atoms 6
CT 12.0110 0.1450 1 0
OH 15.9990 -0.6830 1 1
HO 1.0080 0.4180 1 0
HC 1.0080 0.0400 1 0
HC 1.0080 0.0400 1 0
HC 1.0080 0.0400 1 0
constraints 5
1 2 1.410
1 4 1.090
1 5 1.090
1 6 1.090
2 3 0.945
angles 7
harm 4 1 5 138.0720 107.800
harm 4 1 6 138.0720 107.800
harm 5 1 6 138.0720 107.800
harm 1 2 3 230.1200 108.500
harm 2 1 4 146.4400 109.500
harm 2 1 5 146.4400 109.500
harm 2 1 6 146.4400 109.500
dihedrals 3
cos3 3 2 1 4 0.0000 0.0000 1.8828 0.50 0.50
cos3 3 2 1 5 0.0000 0.0000 1.8828 0.50 0.50
cos3 3 2 1 6 0.0000 0.0000 1.8828 0.50 0.50
finish
vdw 10
CT CT lj 0.276144 3.500000
CT OH lj 0.443188 3.304542
CT HO lj 0.000000 0.000000
CT HC lj 0.186176 2.958040
OH OH lj 0.711280 3.120000
OH HO lj 0.000000 0.000000
OH HC lj 0.298797 2.792848
HO HO lj 0.000000 0.000000
HO HC lj 0.000000 0.000000
HC HC lj 0.125520 2.500000
close
TIP4P/2005 heavy water model
UNITS kJ
MOLECULES 1
TIP4P2005 water
NUMMOLS 4000
ATOMS 4
OW 15.999 0.0000 1 0 1
HW 2.014 0.5564 2 0 1
OM 0.000 -1.1128 1 0 1
RIGID BODIES 1
4 1 2 3 4
FINISH
VDW 1
OW OW lj 0.7749 3.1589
CLOSE
!From Abascal (2005):
!
! V = 4E*((s/r)^12-(s/r)^6) with s = 3.1589 A
! E = 93.2 K = 0.77490787 kJ/mol
!
!Water geometry: d(OH) = 0.9572 A, angle(HOH) = 104.52, d(OM) = 0.1546 A
TIP4P/2005 heavy water model
UNITS kJ
MOLECULES 1
TIP4P2005 water
NUMMOLS 4000
ATOMS 4
OW 15.999 0.0000 1 0 1
HW 2.014 0.5564 2 0 1
OM 0.000 -1.1128 1 0 1
RIGID BODIES 1
4 1 2 3 4
FINISH
VDW 1
OW OW lj 0.7749 3.1589
CLOSE
!From Abascal (2005):
!
! V = 4E*((s/r)^12-(s/r)^6) with s = 3.1589 A
! E = 93.2 K = 0.77490787 kJ/mol
!
!Water geometry: d(OH) = 0.9572 A, angle(HOH) = 104.52, d(OM) = 0.1546 A
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# MDANSE
MDANSE (Molecular Dynamics Analysis for Neutron Scattering Experiments) is a python library/application for analysis molecular dynamics simulation data
This is nMoldyn-3.0.12, an interactive program for the
analysis of Molecular Dynamics trajectories. This program is
copyrighted but free to use for anyone under the CeCILL license,
see the file LICENSE for details.
nMoldyn should work with all major variants of Unix, including Linux
and MacOSX and Windows. There is little system-specific code in nMoldyn
itself, so porting nMoldyn to other systems should be straightforward.
However, we cannot provide any support for this.
If you have any questions about nMoldyn that are not answered on the
Web page mentioned above, please contact the authors.
Eric Pellegrini
Calcul Scientific
Institut Laue Langevin
6 Rue Jules Horowitz
38042 Grenoble
France
E-Mail: pellegrini@ill.fr
Konrad Hinsen
Centre de Biophysique Moleculaire (CNRS)
Rue Charles Sadron
45071 Orleans Cedex 2
France
E-Mail: hinsen@cnrs-orleans.fr
Gerald Kneller
Centre de Biophysique Moleculaire (CNRS)
Rue Charles Sadron
45071 Orleans Cedex 2
France
E-Mail: kneller@cnrs-orleans.fr
Step 1: Prerequesites
=====================
Before installing nMOLDYN make sure that the following components are installed
and configured properly:
-Tcl and Tk libraries version >= 8.4
-Python 2.4 or higher
-numpy version >= 1.2
-matplotlib version >= 0.98
-pyro version >= 3.9
-Scientific version >= 2.8
-MMTK version >= 2.6.1
-NetCDF library version >= 3.6.1
To check for that, in a terminal, type
python -c 'import Scientific.IO.NetCDF'
If you get no error message NetCDF is likely to be properly installed and
configured on your system.
Step 2: installation
====================
In a terminal, type the following instructions in the directory where you untared
the nMOLDYN archive:
cd nMOLDYN-3.X.Y
python setup.py build
python setup.py install
The last command may require administrator privileges.
Step 3: running nMOLDYN
=======================
Once the installation is completed run nMOLDYN by typing
./nMOLDYNStart.py
in your Python binaries directory.
In the future, you should create an alias/shortcut for that script in order to not
disrupt any component of that sensitive directory.
WARNING:
========
If the version of Scientific used to run nMOLDYN is the 2.9.0, small changes has
to be performed in order to use nMOLDYN in parallel mode via a Pyro server.
The changes are the following:
FILE : MasterSlave.py
LOCATION: Scientific installation directory
REPLACE
def getMachineInfo():
import os
sysname, nodename, release, version, machine = os.uname()
pid = os.getpid()
return "PID %d on %s (%s)" % (pid, nodename, machine)
BY
def getMachineInfo():
import os
import platform
sysname, nodename, release, version, machine, processor = platform.uname()
pid = os.getpid()
return "PID %d on %s (%s)" % (pid, nodename, machine)
If you are not familiar with the Python installed modules file structure, you
can find the path for Scientific directory by running the following command
within the Python interpreter:
import Scientific
print Scientific.__path__[0]
KNOWN BUGS:
===========
- Bug with tk >= 8.5 on Linux (Fedora, Suse, Ubuntu): when using a tkMessageBox, if you click 'Yes'
the answer will be the same as 'No'! In nMOLDYN, you will experience this bug at the end of an
analysis when you can decide to plot the results just after the analysis. Whatever is your decision
('Yes' or 'No'), no plot will be displayed.
Here is the proposed patch (http://bugs.python.org/issue4961):
Index: Lib/lib-tk/tkMessageBox.py
===================================================================
--- Lib/lib-tk/tkMessageBox.py (revision 73494)
+++ Lib/lib-tk/tkMessageBox.py (working copy)
@@ -70,11 +70,13 @@
if title: options["title"] = title
if message: options["message"] = message
res = Message(**options).show()
- # In some Tcl installations, Tcl converts yes/no into a boolean
+ # In some Tcl installations, yes/no is converted into a boolean.
if isinstance(res, bool):
- if res: return YES
+ if res:
+ return YES
return NO
- return res
+ # In others we get a Tcl_Obj.
+ return str(res)
def showinfo(title=None, message=None, **options):
"Show an info message"
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