Previous Thread
Next Thread
Print Thread
#18729 08/14/08 07:34 PM
Joined: Jan 2005
Posts: 127
P
preeti Offline OP
Forum Member
OP Offline
Forum Member
P
Joined: Jan 2005
Posts: 127
Hello,

Is there a script to compute molecular mechanics entropy using CHARMM from a trajectory?

Thanks,
Preeti

Joined: Sep 2003
Posts: 4,861
Likes: 10
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,861
Likes: 10
Use the QUASiharmonics command in the VIBRAN module (vibran.doc).
Note that you need a fairly long trajectory for this to converge, and you have to remove overall translation/rotation from the trajectory first, then something like this would get you the quasiharmonic entropy:

coor dyna firstu 51 nunit 1 begin 500 stop 1000000 skip 500 sele segid prot end
calc nmodes = 3 * ?NSEL
bomlev -2 ! we will go beyond the deault limit of 3600 modes
vibran nmode @nmodes
quasi firstu 51 nunit 1 begin 500 stop 1000000 skip 500 sele segid prot end -
thermo resi temp 300


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.008s Queries: 18 (0.005s) Memory: 0.7275 MB (Peak: 0.7676 MB) Data Comp: Off Server Time: 2022-12-04 21:58:44 UTC
Valid HTML 5 and Valid CSS