Linker IT Software
Google
Web www.oraxcel.com
menubar-top-links menubar-top-rechts
Home Help Search Login
Welcome, Guest. Please Login.
SQL*XL: Database to Excel bridge litLIB: Excel power functions pack ExcelLock: Locking and securing your valuable Excel spreadsheets encOffice: Protect your Excel file easy and safe encOffice: Protect your Excel file easy and safe
Pages: 1
MD with DRF90 (Read 2242 times)
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
MD with DRF90
25.04.10 at 18:58:19
 
MD with DRF90
 
MD, Molecular Dynamics, calculations can be performed with DRF90.
 
For practical help please read:
DRF90: Molecular Dynamics (MD) calculations  
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1251641181/0#3
 
When starting an MD calculation the system is should be run from its initial configuration for a period of time until the ensamble average of the enthalpy of the system has stabilised. While the run progresses statistical information is collected. However after this startup phase the statistical information should be thrown away as it also contains information collected when the system was not yet in equilibrium. A new start should be made from the equilibrium configuration so statistical information can be gathered from a single Bolzmann distribution. To restart the .drf90data file is needed, the nxsteps parameter should be increased and drf90 should be called with the -d flag: drf90 -d jobfile
 
The output of a MD simulation is the DRF90 output file and a separate simulation data or SIMDATA file can be created. Using Marcel Swart's Converter utility msc (http://iqc.udg.es/~marcel/eng/msc/index.html) this file can be converted to e.g. a movie-pdb file.
 
Example to create a .pdb file from the SIMDATA output:
msc -i drf.out -it drfout -ot movpdb -o drf.pdb
This commands takes the drf.out output file (it finds the drf.SIMDATA file by itself) and converts it into the drf.pdb file.
 
There are a few programs that can be used to view the movie. PYMOL is one of them. Simply read the pdb file into the program. Rotate the molecule and use the slice and zoom tools to view the part of the system that interests you most and then save the movie into a movie file (MPEG).
 
See also:
Molecular Mechanics & Molecular Dynamics
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1228392226
DRF90: Molecular Dynamics (MD) calculations  
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1251641181/0#3
Marcel Swart's Converter
http://iqc.udg.es/~marcel/eng/msc/index.html
Back to top
 
« Last Edit: 02.06.10 at 14:17:43 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Gerrit-Jan Linker
YaBB Administrator
*****




Posts: 75
DRF90:MD Restart MD
Reply #1 - 02.06.10 at 14:24:33
 
DRF90:MD Restart MD
 
To restart an MD simulation with DRF90 you need to call drf90 with the -d option:
drf90 -d inputfile
 
The drf90data file needs to be available from the last run.
 
The number of steps (nrsteps) in the input file should be increased.
 
When correctly it should pick up the last configuration from the drf90data file however at the moment it does not seem to do that. Manually the geometry of the last simulation step needs to be copied to the input file.
Back to top
 
 

Gerrit-Jan Linker
Linker IT Software
Email WWW Gerrit-Jan Linker   IP Logged
Pages: 1