Re: extracting force on a single atom

From: Ben Adams (benny.adams1993_at_gmail.com)
Date: Thu Aug 31 2017 - 08:38:05 CDT

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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