Hi Peter,
This is the config file with
minimize:
#############################################################
## EXECUTION SCRIPT
##
#############################################################
#Minimization
if {0} {
minimize
10000
reinitvels $temperature
}
and this is the config file with minimization on
command:
minimization on
if {0} {
minimize
20000
reinitvels $temperature
}
I would like to run MD with periodic boundary
conditions and PME. If I use restart files the boundary conditions are read by the .xsc file? SO I can omit periodic boundary conditions information
but I have to specify PME information in the config file?
thanks
Roberta
On Mon, 11 May 2009 12:11:57 -0500
Peter
Freddolino <petefred@ks.uiuc.edu> wrote:
> Hi Roberta,
>
> roberta.rostagno wrote:
>> Thank you for your answer. If
I don't use minimization
>>on, but only
>> minimize command after few steps I have the error:
>> bad global exclusion
clount. Instead with minimization
>> on the
>> minimization run without errors until the end.
>
> I can't think of any
reason for minimize n and
>minimization on; run n to
> yield different results... could you send me snippets of
>the end of
the
> relevant config files?
>
> Bad global exclusion count errors generally indicate an
>overly long bond
> in the
system... can you visually inspect your structure
>and make sure
> it looks ok?
>
> By the way, is namd terminating upon the
exclusion count
>error? During
> minimization, bad global exclusion counts should give a
>warning but not
> an
error.
>
>> if I run minimization and MD with different conf file,
>>can I use restart
>> coordinate and velocity
files obtained from minimization
>>to start MD?
>> thanks again for help
>
> Yes; you can read the coordinates,
velocities, and
>extended system from
> the previous run with bincoordinates, binvelocities, and
>extendedSystem,
>
respectively (they'll be named
>$outputname.restart.coor/vel/xsc)
>
> By the way, are you sure you mean to be running without
>pme?
> Also, that rigid bond tolerance is quite large...
>
> Best,
> Peter
>