Re: extracting force on a single atom

From: Ben Adams (benny.adams1993_at_gmail.com)
Date: Thu Aug 31 2017 - 10:03:04 CDT

Thank you very much.
Just for last question, when I use this command in my tclforces script,
either inside calcforces or just inside tclForces, I get this error message:

FATAL ERROR: unknown parameter

    while executing

"getsetp"

    invoked from within

"set t [getsetp]"

I'm using NAMD 2.11.

Best,

Ben

On Thu, Aug 31, 2017 at 8:46 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> What you need to do is define the script from the beginning, but do
> nothing on the first timestep - at least not call loadtotalforces. You can
> use [getstep] to keep track of the timestep.
>
> Jerome
>
>
> On 31 August 2017 at 15:38, Ben Adams <benny.adams1993_at_gmail.com> wrote:
>
>> Thank you. So if I somehow avoid loadTotalForces at the very first
>> timestep my problem will be solved? Do you have any suggestions?
>> I tried to run for 20 steps and then added my tclForces script but it
>> failed:
>>
>> FATAL ERROR: Setting parameter tclForces from script failed!
>>
>>
>> On Thu, Aug 31, 2017 at 5:37 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>> wrote:
>>
>>> Hi Ben,
>>>
>>> Two things here. The first one is, you probably want to use
>>> loadTotalForces rather than loadForces (loadforces will only collect
>>> external forces applied through TclForces). Second, with loadTotalForces,
>>> data is collected at the end of one timestep and available on the next. So
>>> no data will be available on the very first timestep, and then the forces
>>> you'll get will be stale by one timestep.
>>>
>>> Best,
>>> Jerome
>>>
>>> On 31 August 2017 at 02:18, Ben Adams <benny.adams1993_at_gmail.com> wrote:
>>>
>>>> Dear NAMD users,
>>>>
>>>> I've been looking everywhere to find a way to extract forces on a
>>>> single atom. It seems the best way is to use "tclforces". Here is that part
>>>> of my NAMD configuration file:
>>>>
>>>> tclForces on
>>>> tclForcesScript {
>>>> set nter [addgroup {3}]
>>>> set cter [addgroup {4}]
>>>> proc calcforces {} {
>>>> global nter cter
>>>> loadcoords coor
>>>> loadforces forces
>>>> print nter=$forces($nter)
>>>> print nter=$coor($nter)
>>>>
>>>> }
>>>> }
>>>>
>>>>
>>>> Unfortunately it doesn't recognize "loadforces" and I get the following
>>>> error:
>>>>
>>>> FATAL ERROR: can't read "forces(g1)": no such variable
>>>> while executing
>>>> "print nter=$forces($nter)"
>>>> (procedure "calcforces" line 5)
>>>>
>>>> I also tried "$forces(4)" and got the same error.
>>>> I search through mailing list. Such a problem is being reported several
>>>> times but there are no answers to them.
>>>> Can anybody help me with that?
>>>> Is there any other way beside "dcdforces" (which outputs all the atoms
>>>> together) to get forces for a single atom?
>>>>
>>>> Regards,
>>>>
>>>> Ben
>>>>
>>>>
>>>
>>
>

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