[gmx-users] pull.ppa doesn't work

[accomp lin]

Problem solved, thanks a lot!








accomp lin wrote:
> <http://www.mdbbs.org/tag-pull.html>
> hi everyone,
> 
> I;m using umbrella sampling to calculate PMF
> 
> My system is DPPC + water + protein
> In pull.ppa, I set runtype = umbrella ，reftype = com_t0，
> K1   = 5000  ，Pos1  = 0.0 0.0 6.0
> 
> However this came out when I finally type mdrun :
>  
> Reading parameter file pull.ppa
> ' for variable verbose, using 'no'
> Next time use one of : 'no' 'yes'
> ' for variable runtype, using 'afm'
> Next time use one of : 'afm' 'constraint' 'umbrella'
> ' for variable reftype, using 'com'
> Next time use one of ; 'com' 'com_t0' 'dynamic' 'dynamic_t0'
> .....................
> .....................
> .....................
>  

Then something is badly formatted in the file.  Perhaps it was edited on a Windows machine and has hidden formatting characters?

> ——————————————————————————————
> program mdrun, VERSION 3.3.3
> source code file: pullinit.c, line: 215
> 
> Fatal error:
> in the index fileGN
> ——————————————————————————————
> 
> It seems that mdrun doesn't recognize what I set in pull.ppa
> And I don't know what's wrong with my index file, it looks all right to me.
> So, can any body tell me what is going on?

Could also be related to the same formatting issues you're seeing with your .ppa file.

-Justin

>  Thanks!
> 
> 
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-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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