Re: dummyAtom in distance colvar in ABF calculations

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Mon May 14 2018 - 12:37:20 CDT

Hi Giacomo,

I attempted to submit the job with dummy atom and oneSiteTotalForce options
and my job quits with the "Global exclusion count" error. I have also
submitted the same system for simple equilibration (i.e. no colvar and no
ABF) and it proceeds without errors, hence there is no problem with
geometry (i.e. no atoms overlapping etc.). Is it possible that dummy atom
creates such error and how can I remove this problem?

Olga

On Mon, May 14, 2018 at 11:26 AM Olya Kravchenko <ovkrav_at_gmail.com> wrote:

> 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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