Re: ERROR: Multiple definitions of 'LangevinPiston'

From: roberta.rostagno (roberta.rostagno_at_unimib.it)
Date: Tue May 12 2009 - 03:02:45 CDT

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
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:56 CST