Re: tclforces: switch from md with external forces to standard md

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jan 09 2009 - 10:46:05 CST

It either needs to be changed to the more intuitive behavior that Vlad
expected or clearly documented; given that the behavior has been this
way for some time, I'm wary of changing it because we might break
current tclforces scripts (the advantage of the current approach is that
it makes life easier if you want to repeatedly apply the same forces for
some reason). It looks like the current behavior stems from the fact
that GlobalMaster only pushes out new forces if they've been changed,
and otherwise leaves them constant (this is beneficial for cases where
constant forces are being applied because it reduces communication). Of
course this could be changed for tclforces pretty easily. I'll talk to
Jim and make sure one or the other happens.

Best,
Peter

Jerome Henin wrote:
> Hi all,
>
> On Thu, Jan 8, 2009 at 2:38 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
>> Hi Vlad,
>> the forces are not cumulative, but they may persist until changed.
>>
>
> One may or may not call this a bug, but... what would it cost to fix it?
>
> Best,
> Jerome
>
>
>
>> Adding a zero force to each atom when you want to turn off the forces
>> should fix things.
>> Best,
>> Peter
>>
>> Vlad Cojocaru wrote:
>>
>>> Dear namd users,
>>>
>>> I have another question regarding tclforces.
>>>
>>> I would like that my tcl script switches at specific intervals between
>>> simulation with external forces and standard md simulation.
>>> So, I introduced a flag and invoked the "addforce" command only if the
>>> flag is defined. After each stint with external forces, I unset the
>>> flag and reset it after the standard md steps.
>>>
>>> However, I noticed that once the switch occurs, the external force
>>> does not disappear. In fact the value given by loadforces command
>>> stays constant during the standard md part and equals the last value
>>> from the part with external forces. From the trajectory, I guess that
>>> the external force is still being applied on my system even during the
>>> desired standard md simulation part.
>>>
>>> Am I right here? Does "addforce" actually adds up forces added at each
>>> time step ?
>>> If yes, is it possible to alter this behavior and reset the external
>>> force to 0 after specific intervals ?
>>>
>>> Thanks for answering
>>>
>>> Merry Christmas and Happy New Year to all of you.
>>>
>>> Vlad
>>>
>>>
>>

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