From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue May 12 2009 - 06:41:29 CDT
Hi Roberta,
could you include a little more context, say, up through the first "run"
statement that you think should be doing dynamics? From what I see here,
it looks like in the first case you're not doing any minimization at all
due to the if statement, which would certainly explain a bad global
exclusion count (or several other errors that boil down to starting
dynamics from a badly strained conformation).
Peter
roberta.rostagno wrote:
> 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 $temperature
> }
> I would like to run MD with periodic boundary conditions and PME. If I
> use restart files the boundary conditions are read by the .xsc file? SO
> I can omit periodic boundary conditions information but I have to
> specify PME information in the config file?
>
> thanks
>
> Roberta
>
> On Mon, 11 May 2009 12:11:57 -0500
> Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>> Hi Roberta,
>>
>> roberta.rostagno wrote:
>>> Thank you for your answer. If I don't use minimization
>>>on, but only
>>> minimize command after few steps I have the error:
>>> bad global exclusion clount. Instead with minimization
>>> on the
>>> minimization run without errors until the end.
>>
>> I can't think of any reason for minimize n and
>>minimization on; run n to
>> yield different results... could you send me snippets of
>>the end of the
>> relevant config files?
>>
>> Bad global exclusion count errors generally indicate an
>>overly long bond
>> in the system... can you visually inspect your structure
>>and make sure
>> it looks ok?
>>
>> By the way, is namd terminating upon the exclusion count
>>error? During
>> minimization, bad global exclusion counts should give a
>>warning but not
>> an error.
>>
>>> if I run minimization and MD with different conf file,
>>>can I use restart
>>> coordinate and velocity files obtained from minimization
>>>to start MD?
>>> thanks again for help
>>
>> Yes; you can read the coordinates, velocities, and
>>extended system from
>> the previous run with bincoordinates, binvelocities, and
>>extendedSystem,
>> respectively (they'll be named
>>$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
>>
>
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