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: Tue Sep 07 2010 - 15:31:07 CDT

Actually I had tried different combinations in atom definition part. None of
them work well.

(1) "psfSegID A A B B C C D D" and then 8 instances of
"atomNameResidueRange".
(2) "psfSegID A A B B C C D D" and then 2 instances of
"atomNameResidueRange".
(3) 8 instances of "atomNameResidueRange" and then "psfSegID A A B B C C D
D".
(4) 2 instances of "atomNameResidueRange""psfSegID A A B B C C D D".

If I just specify 2 instances of atomNameResidueRange, 236 atoms can be
selected (that is the number of atoms on each segment). But when 8 instances
of atomNameResidueRange is assigned, then 237 atoms will be defined. I do
not know where does this additional atoms come from.

On Tue, Sep 7, 2010 at 12:23 PM, Giacomo Fiorin
<giacomo.fiorin_at_temple.edu>wrote:

> Did you specify only two instances of atomNameResidueRange? If that's
> case, no wonder that segments B, C and D were ignored.
>
>
> 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 6:26 PM, dhacademic <dhacademic_at_gmail.com> wrote:
>
>> Hi Jerome and Giacomo,
>>
>> I have tried the following syntax (in colvars.conf file) according to the
>> reply:
>> atoms {
>>
>> psfSegID A A B B C C D D
>> atomNameResidueRange CA 386-485
>> atomNameResidueRange CA 628-763
>> }
>> And I still meet a similar output shown as follow. This time 236 atoms on
>> segment A can be selected. However, the rest atoms on segment B, C, D are
>> still ignored. It looks like that this atom definition error comes from to
>> the bug of the version 2.7b1.
>>
>> #### my output file ####
>> ....
>> colvars: Initializing atom group "atoms".
>> colvars: Warning: found more than one instance of "psfSegID".
>> colvars: Atom group "atoms" defined, 236 atoms, total mass = 2834.6.
>>
>> colvars: # refPositionsFile = colvarb.pdb
>> colvars: # refPositionsCol = B
>> colvars: # refPositionsColValue = 1
>> colvars: Error: the PDB file "colvarb.pdb" contains coordinates for
>> only 87342 atoms, but 236 are needed.
>> .....
>>
>> 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).
>>>>> What
>>>>> > is wrong with my syntax?
>>>>>
>>>>> Not sure. What version of NAMD are you using? I wonder if this could
>>>>> be an old bug that is now fixed.
>>>>>
>>>>> Cheers,
>>>>> Jerome
>>>>>
>>>>
>>>>
>>>
>>
>

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