Re: Parameter colvars

From: Z (shenzldlut_at_gmail.com)
Date: Mon Oct 06 2014 - 06:55:44 CDT

Yes, you are right! I wrote the colvar configuration file in Windows 7
by Notepad++, and run NAMD in SUSE Linux.I will try to use dos2unix.
Another, I have a problem, I used NAMD without problem,so this error
just happen in colvar?
Thank you!

Z
E-mail:shendlut_at_gmail.com

在 2014/10/6 19:02, Branko 写道:
> Z,
>
> Did you make colvar configuration file in Windows and run NAMD in
> LInux. If so, program most probably did not recognize end of lines in
> colvar configuration file. You can use dos2unix
> (http://dos2unix.sourceforge.net/) to convert ends of lines, or simply
> use some text editor with the same functionality (ProgramersNotePad or
> similar)
>
> Branko
>
>
> On 10/6/2014 12:56 PM, Z wrote:
>> The colvars configuration as a separate file(.in format).In my NAMD
>> config file ,the colvers is been written like this:
>>
>> colvars on
>> colvarsConfig Distance.in
>>
>> firsttimestep 22000
>> run 2000000
>> Z
>> E-mail:shendlut_at_gmail.com
>> 2014/10/6 18:45, Giacomo Fiorin:
>>>
>>> Do you supply the colvars configuration as a separate file or as
>>> part of the NAMD configuration file?
>>>
>>> On Oct 6, 2014 6:26 AM, "Z" <shenzldlut_at_gmail.com
>>> <mailto:shenzldlut_at_gmail.com>> wrote:
>>>
>>> Dear all,
>>> I want to use ABF to calculate PMF,so I am running simulation
>>> with colvars. However, the NAMD2.8 said :
>>>
>>> TCL: Setting parameter colvars to on
>>> FATAL ERROR: Setting parameter colvars from script failed!
>>>
>>> FATAL ERROR: Setting parameter colvars from script failed!
>>>
>>> FATAL ERROR: Setting parameter colvars from script failed!
>>>
>>> FATAL ERROR: Setting parameter colvars from script failed!
>>>
>>> FATAL ERROR: Setting parameter colvars from script failed!
>>>
>>> my colvars flie :
>>> colvarsTrajFrequency 100
>>> colvarsRestartFrequency 1000
>>>
>>> colvar {
>>> name IonDistance
>>>
>>> width 0.1
>>>
>>> lowerboundary -45.6
>>> upperboundary 45.6
>>>
>>> lowerWallConstant 10.0
>>> upperWallConstant 10.0
>>>
>>> distanceZ {
>>> main {
>>> atomsFile ./main_atom.pdb
>>> atomsCol B
>>> atomsColValue 1.0
>>> }
>>> ref {
>>> atomsFile ./ref_atom_2.pdb
>>> atomsCol O
>>> atomsColValue 1.0
>>> }
>>> }
>>> }
>>>
>>> abf {
>>> colvars IonDistance
>>> fullSamples 100
>>> hideJacobian
>>> }
>>>
>>> I want to know which parameter has problem?
>>> Thanks!
>>>
>>> P.S.
>>> There are tclForces parameters in my conf flie.
>>>
>>> --
>>> Z
>>> E-mail:shendlut_at_gmail.com <mailto:shendlut_at_gmail.com>
>>>
>>
>

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:54 CST