Re: FATAL ERROR: Setting parameter colvars from script failed!

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Sep 30 2014 - 13:04:27 CDT

Do you have several instances of "colvars" in your NAMD config file?

Jerome

On 30 September 2014 19:56, Mihaela Drenscko <quo.physics_at_gmail.com> wrote:

> It is NAMD 2.9. Before I run simulations of PCL in water with colvars and
> I didn't have this problem. What can I do about it?
> Mihaela
>
> On Tue, Sep 30, 2014 at 11:17 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> Are you perhaps using a very old version of NAMD? One that didn't have
>> the colvars feature yet? At the top of NAMD's output, you'll find the
>> version information.
>>
>> Best,
>> Jerome
>>
>> On 30 September 2014 16:27, Mihaela Drenscko <quo.physics_at_gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I am running a simulation of PS in a solvent with colvars. In the
>>> output file I get this error:
>>>
>>> TCL: Setting parameter colvars to on
>>>
>>> FATAL ERROR: Setting parameter colvars from script failed!
>>>
>>>
>>>
>>> This is the colvars script:
>>>
>>>
>>>
>>> colvarsTrajFrequency 100
>>>
>>> colvarsRestartFrequency 10000
>>>
>>>
>>>
>>> colvar {
>>>
>>> name rgyr1
>>>
>>>
>>>
>>> width 0.5
>>>
>>> lowerBoundary -2.0
>>>
>>> upperBoundary 15.0
>>>
>>> lowerWallConstant 150.0
>>>
>>> upperWallConstant 150.0
>>>
>>>
>>>
>>> gyration {
>>>
>>> atoms {
>>>
>>> atomsFile ../testmod.pdb
>>>
>>> atomsCol B
>>>
>>> atomsColValue 1.0
>>>
>>> }
>>>
>>>
>>>
>>>
>>>
>>> }
>>>
>>> }
>>>
>>>
>>>
>>> metadynamics {
>>>
>>> colvars rgyr1
>>>
>>> hillWeight 0.1 0.1
>>>
>>> newHillFrequency 100 100
>>>
>>> hillWidth 2.0 2.0
>>>
>>> useGrids on
>>>
>>> dumpFreeEnergyFile on
>>>
>>> saveFreeEnergyFile on
>>>
>>> }
>>>
>>>
>>> And this is how testmod.pdb looks like:
>>>
>>> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
>>>
>>> ATOM 1 CG PSH P 0 5.126 90.084 76.320 1.00 1.00
>>> PS C
>>>
>>> ATOM 2 CD1 PSH P 0 5.369 91.296 75.819 1.00 1.00
>>> PS C
>>>
>>> ATOM 3 HD1 PSH P 0 6.190 91.862 76.175 1.00 1.00
>>> PS H
>>>
>>> etc...
>>> What is wrong and how do I fix it?
>>> Thank you,
>>> Mihaela
>>>
>>
>>
>

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