Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs.

From: dhacademic (dhacademic_at_gmail.com)
Date: Wed Sep 08 2010 - 16:46:37 CDT

Now I am using 2.7b3. However, the old problem remains unresolved, and new
problem appears again, which makes me feel really frustrated. The full
colvars.conf file is as below:

colvar {
name dist1colvar
outputSystemForce yes
outputAppliedForce yes
distance {
    group1 {
        atomNumbers { 100969 }
    }
    group2 {
        atomNumbers { 94228 }
    }
}
}

colvar {
name dist2colvar
outputSystemForce yes
outputAppliedForce yes
outputvalue off
distance {
    group1 {
        atomNumbers { 107518 }
    }
    group2 {
        atomNumbers { 87679 }
    }
}
}

colvar {
name rmsdcolvar
outputSystemForce yes
outputAppliedForce yes
outputvalue off
rmsd {
    atoms {
# psfSegID A A B B C C D D
        psfSegID A
        atomNameResidueRange CA 386-485
# atomNameResidueRange CA 628-763
# atomNameResidueRange CA 386-485
# atomNameResidueRange CA 628-763
# atomNameResidueRange CA 386-485
# atomNameResidueRange CA 628-763
# atomNameResidueRange CA 386-485
# atomNameResidueRange CA 628-763
    }
    refPositionsFile colvarn.pdb
    refPositionsCol B
    refPositionsColValue 5.0
}
}

harmonic {
name distbias
colvars dist1colvar dist2colvar
centers 3.5 3.5
forceConstant 10.0
}

harmonic {
name rmsdbias
colvars rmsdcolvar
centers 1.46569
targetcenters 0.0
targetNumSteps 8000
targetforceConstant 1000.0
}

The problems are:

(1) if I specify "psfSegID A A B B C C D D" and the corresponding 8
instances of "atomNameResidueRange", 237 atoms will be defined. In fact the
total atoms should be 236*4=944;

(2) if I sepcify "psfSegID AD" and the corresponding 1 instance of
"atomNameResidueRange", 100 atoms will be defined. It's OK up to now. Then I
meet the following error message after the atom selection:

colvars: Initializing a new "harmonic" instance.
colvars: # name = rmsdbias
colvars: # colvars = { rmsdcolvar }
colvars: # forceConstant = 1 [default]
colvars: # centers = { 1.46569 }
colvars: # targetCenters = { 0 }
colvars: # targetForceConstant = 1000
colvars: Error: cannot specify both targets and forceConstantTarget.
colvars: If this error message is unclear, try recompile with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.

I think I do not specify any other "targets" besides my rmsdcolvar. Can
anyone help me to figure out the above problems? Any suggestion is
appreciated!

Best,

Hao

On Mon, Sep 6, 2010 at 3:10 PM, Giacomo Fiorin <giacomo.fiorin_at_temple.edu>wrote:

> It would be best to use 2.7b2 or 2.7b3, in general.
>
> In the specific example, you used four psfSegID values but you specified
> them separately: the correct syntax is to put them on the same line (one
> psfSegID keyword with multiple values).
>
> Also, there may be only one atomNameResidueRange option for each psfSegID
> value, not two of them as in your case. You should use something like
> "psfSegID A A B B C C D D" to fix this.
>
> Giacomo
>
>
> ---- ----
> Dr. Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science - Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> giacomo.fiorin_at_temple.edu
> ---- ----
>
>
>
>
> On Mon, Sep 6, 2010 at 11:29 AM, dhacademic <dhacademic_at_gmail.com> wrote:
>
>> my version is NAMD 2.7b1
>>
>>
>>
>> On Mon, Sep 6, 2010 at 11:14 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
>>
>>> Hi,
>>>
>>> First, for TMD, you probably need the restraint force, so you should
>>> request outputAppliedForce, not outputSystemForce.
>>>
>>>
>>> > (1) Do the "centers" and "targets" keywords mean the initial and final
>>> RMSD
>>> > of the system? I feel confused by reading the related part of the
>>> > user-manual.
>>>
>>> They are the initial and final values of the center of the restraint
>>> potential. If all goes well, the RMSD should follow.
>>>
>>>
>>> > (2) I want to define 4 (segments) * 236 (per segment) = 944 atoms in
>>> the
>>> > input. However, only 237 atoms are defined according to the output
>>> > file. Someone else used a similar way to define atoms within different
>>> > segments
>>> > (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12359.html)--0016364d2fcbb2568d048fc67230--

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