Re: torsional restrain

From: Lara rajam (lara.4884_at_gmail.com)
Date: Thu Feb 23 2017 - 15:23:31 CST

Dear NAMD

I have moved the extra bond before minimization it is not working giving
high energy values during minimization

Warning: Low global exclusion count! (11925 vs 28234)

Warning: This warning is not unusual during minimization.

Warning: Increasing pairlistdist or cutoff may avoid this.

ENERGY: 44 4081237657.1245 158669.7190 9999999999.9999
504.0990 -3035.6460 553.1592 169.0763 0.0000
      0.0000 9999999999.9999 0.0000 9999999999.9999
9999999999.9999 0.0000 9999999999.9999 9999999999.9999
211932.0000 9999999999.9999 9999999999.9999

could you suggest me where is the issue, this will help me a lot thank you

On Thu, Feb 23, 2017 at 1:02 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Wait, this is after a run command? That is the problem. :) There are
> certain things you can adjust after the first run or minimization command
> is issued, and adding extrabonds isn't one of them. Push the extrabonds
> specifications above your first run/minimize statement.
>
> -Josh
>
> On 02/23/2017 10:56 AM, Lara rajam wrote:
> Dear Joshua !
> Thank you , for the reply ..
> I have changed the file name but, still I get the error message. I moved
> the restrain file next to minimization steps
> and the res.txt is in the same path
> the error is as below
>
> The last position output (seq=-1) takes 0.004 seconds, 23.830 MB of memory
> in use
>
> WRITING VELOCITIES TO OUTPUT FILE AT STEP 4000
>
> The last velocity output (seq=-1) takes 0.001 seconds, 23.581 MB of memory
> in use
>
> TCL: Setting parameter extraBonds to on
>
> FATAL ERROR: Setting parameter extraBonds from script failed!
>
>
> FATAL ERROR: Setting parameter extraBonds from script failed!
>
>
> Is there any suggestions to fix this thank you
>
>
> On Thu, Feb 23, 2017 at 12:09 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov
> <mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
> Hi Lara,
>
> A few things spring to mind that might be simple fixes, since the syntax
> looks right:
>
> 1.) I recall some parameters in NAMD being case-sensitive. In the manual,
> its extraBonds and extraBondsFile.
> 2.) Make sure the res.txt is in the right place. Should be in the same
> directory as the .conf/.namd file.
>
> -Josh
>
> On 02/23/2017 09:19 AM, Lara rajam wrote:
> Dear NAMD
>
> I would like to use the torsional restraint in the simulation. I went
> through the manual. This is my first time of adding restraints
> and added
>
>
> extrabonds on
>
> extrabondsfile res.txt
>
>
> in the configuration file.
>
>
> the file contents are below
>
>
> dihedral 2048 2053 2060 2064 1.0 53.86
>
> dihedral 2053 2060 2064 2050 1.0 -54.78
>
> dihedral 2060 2064 2050 2052 1.0 58.51
>
> dihedral 2064 2050 2052 2048 1.0 -62.73
>
>
> but after minimization the run is not going with saying an error
>
>
> Reason: FATAL ERROR: Setting parameter extrabonds from script failed!
>
>
>
> Fatal error on PE 2> FATAL ERROR: Setting parameter extrabonds from script
> failed!
>
>
>
> Could someone let me know what the error is where I am doing a mistake, I
> have also a question regarding the k spring constant value, how to specify
> 1.0 or 2.0
>
> thanks
>
>
>
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:07 CST