Re: dummyAtom in distance colvar in ABF calculations

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Mon May 14 2018 - 10:26:55 CDT

Hi Giaocomo,

thank you, I have added the oneSiteTotalForce option, now the distance
colvar looks this way:

distance {
      oneSiteTotalForce
      group1 {
         atomnumbers { 66462 }
      }
      group2 {
         dummyAtom (1.485 -0.486 -0.418) }
   }
}

Is this the right place and syntax for this option?

Thank you!

Olga

On Sun, May 13, 2018 at 11:17 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hi Olga, the error message:
> *colvars: Error: total total forces are not available from a dummy atom
> group.*
> should be self-explanatory.
>
> You should set up the "distance" component such that the total force is
> not computed from the dummy group:
>
> https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_distance
>
> On Sat, May 12, 2018 at 5:44 PM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>
>> Hi all,
>>
>> I am using distance colvar for ABF calculations and I want to use
>> dummyAtom for my group 2 atoms that coincides with the COM of the protein
>> (instead of calculating COM of the whole protein every step). I am getting
>> the following error:
>>
>> colvars: Errcolvars: Error: total total forces are not available from a
>> dummy atom group.
>> colvars: No such file or directory
>> FATAL ERROR: Error in the collective variables module: No such file or
>> directory
>> or: total total forces are not available from a dummy atom group
>>
>> Here is my .in file:
>>
>> colvarsTrajFrequency 500
>> colvarsRestartFrequency 5000
>>
>> colvar {
>> name IonDistance
>>
>> width 0.1
>>
>> lowerboundary 70.0
>> upperboundary 74.0
>>
>> lowerwallconstant 100.0
>> upperwallconstant 100.0
>>
>> distance {
>> group1 {
>> atomnumbers { 66462 }
>> }
>> group2 {
>> dummyAtom (1.485 -0.486 -0.418) }
>> }
>> }
>>
>> abf {
>> colvars IonDistance
>> fullSamples 500
>> hideJacobian
>> }
>>
>> Is this the right way to refer to the dummyAtom? I would appreciate your
>> help!
>>
>> Thank you,
>>
>> Olga
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

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