ungebetenergast - 29-3-2004 at 07:43
Are there any freeware molecular dynamics simulation programs for Windows or will I have to set up Linux?
[Edited on 19-4-2004 by chemoleo]
chemoleo - 29-3-2004 at 09:19
I am not aware of many.
I know that Swiss PdB viewer offers energy minimisations, and runs under windows.
Their is partially relevant info on http://www.sciencemadness.org/talk/viewthread.php?tid=1437
Also, have a look at
http://www.ks.uiuc.edu/Research/namd/
However I don't think there are many around, especially for the windows platform.
All those I am aware of are for SGI/Unix/Linux and cost a vast amount of money.
Polverone knows more about this, so let's see what he's got to say 
Polverone - 29-3-2004 at 10:28
Most chemistry software is very expensive unless you are performing research at a university. Then the software may be only somewhat expensive, or
even free in some cases. There are exceptions, though.
It appears that <A HREF="http://www.ks.uiuc.edu/Research/namd/">NAMD</A> is free and has a Windows executable available, and
<A HREF="http://www.ks.uiuc.edu/Research/vmd/">VMD</A> apparently provides some graphical capabilities and works with NAMD.
I would imagine you'll probably be writing some sort of script or description file for NAMD, processing it on the command line, and eventually
getting some sort of output that you can visualize. Programmable, command-line driven software designed by and for other computational chemists seems
to be the most common and least expensive. I would be greatly (though pleasantly) surprised if you found any reasonably powerful, easy to use,
GUI-driven MD software for under $1000.
It appears that NAMD has some GUI-driven aspects, but I can't tell how complete that is from a cursory inspection.
ungebetenergast - 29-3-2004 at 11:55
Thank you both for your response!
I have once used the freeware program GROMACS (gromacs.org) on linux some time ago, but I can't tell if it's good since I have no other
programs of this type (except Rasmol/spdbv-like programs, which don't supply simulation) to compare with. The titel "the world's
fastest ..." is probably exaggerated since I needed 2 days for the simulation of a 30 kDa protein in aqueous solution on a 1400 MGHz computer for
10 picoseconds .
In any case, I will have a look at NAMD.
There are some other MDS/structure prediction-programs (some of them for free) found on this page:
http://www.rcsb.org/pdb/software-list.html
[Edited on 29-3-2004 by ungebetenergast]
TheOrbit - 8-5-2009 at 04:44
all are not free accelyris & molegero .....
linux programs are the only free, but u can still use them in windows using Cygwin appliaction