Re: dummyAtom in distance colvar in ABF calculations

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon May 14 2018 - 18:49:02 CDT

Look into the boundaries.

On Mon, May 14, 2018 at 1:37 PM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:

> 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
>>>
>>

-- 
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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