From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Sep 30 2014 - 13:28:48 CDT
Does it occur after a "run" command? It has to be before the first instance
of "run".
Jerome
On 30 September 2014 20:26, Mihaela Drenscko <quo.physics_at_gmail.com> wrote:
> I have this at the end of config file:
>
> ########################COLVARS###############################
> colvars on
> colvarsConfig rgyr.in
>
>
> On Tue, Sep 30, 2014 at 2:04 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> 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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