NAMD Server Plugin, Version 1.0
Provides an interface for starting NAMD in "server mode". NAMD is started externally and its output is piped back into VMD such that the energy output can be utilized. You can generate a NAMD input file that contains code such that NAMD starts up, opens a socket and goes into waiting mode (event-loop, waiting for socket to be connected). The NAMDserver plugin polls the server and as soon as it's up it will connect a client to it. In the following every line that the client sends to the server will be evaluated in NAMD as a command (TCL and NAMD commands). The results will be sent back to the client through the socket. Thus you can interactively control NAMD.NAMDserver is most useful, if you want to build a structure once and then want to evaluate energies for different coodinates or charges which you generate on the fly through another script. Thus you can save the startup phase of NAMD for the subsequent calculations, if the structure was built once in NAMD.
I prepared two function that simplify life even more:
::NAMDserver::namd_eval will send $cmd to the server and block until the return value is received or the timeout has been reached.
::NAMDserver::namd_compute_energies {sock dcdfile} will request the evaluation of the energies for all frames of the given dcdfile and block until the return value is received or the timeout has been reached. The resulting energies are stored in ::NAMDserver::etitle and ::NAMDserver::energy.
NAMDserver works only in conjunction with namdenergy since you must use the latter is used to build the NAMD input files using the -server flag.
Example:
set sel [atomselect top "segid CWAT"]
namdenergy -sel $sel -bond -server -tempname "namdserver"
-par par_all27_prot_lipid_na.inp
set sock [start_server "namdserver-temp.namd"]
set energy [namd_compute_energies $sock myfile.dcd]
set energy2 [namd_compute_energies $sock myotherfile.dcd]
Author:
Jan Saam
saam@charite.de
