Re: restraint with colvars mocule

From: Ling Wu (emilia.l.wu_at_gmail.com)
Date: Mon Sep 12 2011 - 09:53:21 CDT

Hi Jerome,

Thanks a lot for your reply, I am testing it again according to your suggestion.

I have another question about colvar, so I used 2 colvar restrain to control the water on the top the membrane and the water on the bottom separately. For water with Z coordinate bigger than 0, I tried to keep it in the range of 35 > Z >11, and it works fine. But
for the water with Z coordinate smaller than 0, I want to keep them in the range of -11 > Z > -35, but it did not work, I copied my colvar file below, and the error message is here. Do you know what's going on here?
Thanks a lot!
-------------------------------------------------------------------------------------------
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2011-02-03.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 100 [default]
colvars: # colvarsRestartFrequency = 1000 [default]
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "step6.1_equilbration.colvars.state".
colvars: The final output state file will be "step6.1_equilibration.colvars.state".
colvars: The trajectory file will be "step6.1_equilibration.colvars.traj".
colvars: Error: no collective variables defined.
colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.

------------------------------------------------------------------------------------------

colvar {
  name waterup
  width 0.1
  lowerboundary 11.0
  upperboundary 35.0
  lowerWall 11.0
  upperWall 35.0
  lowerWallConstant 2.5
  upperWallConstant 2.5
  distanceZ {
      main {
         atomsFile watup_main.ref # use Tcl script to generate this file with selection of all the waters #
           atomsCol B
           atomsColValue 1.0
       }
      ref {
         dummyAtom ( 0.000, 0.000, 0.000 )
       }
        axis (0.0, 0.0, 1.0)
  }
}

colvar {
  name waterdown
  width 0.1
  lowerboundary -35.0
  upperboundary -11.0
  lowerWall -35.0
  upperWall -11.0
  lowerWallConstant 2.5
  upperWallConstant 2.5
  distanceZ {
      main {
         atomsFile watdown_main.ref # use Tcl script to generate this file with selection of all the waters #
           atomsCol B
           atomsColValue 1.0
       }
      ref {
         dummyAtom ( 0.000, 0.000, 0.000 )
       }
        axis (0.0, 0.0, 1.0)
  }

Emilia
On Sep 12, 2011, at 4:48 AM, Jérôme Hénin wrote:

> Hi Emilia,
>
> From your input, one would expect the center of the whole membrane to
> shift to z=19 A eventually. To achieve what you want, you need two
> variables, one for each leaflet, and restrain one to +19 and the other
> to -19.
>
> Cheers,
> Jerome
>
> On 11 September 2011 23:25, Ling Wu <emilia.l.wu_at_gmail.com> wrote:
>> Hi All,
>>
>> I have a question regarding the colvars function of NAMD.
>>
>> I am trying to run a simulation of a pure POPC membrane system. I want to enforce a positional restrain on the head group and the tail group of POPC to constrain them at a certain area along Z-axis for the initial equilibration. After I apply this restrain on the system, I checked if the center of mass of the head group or tail group is in the area I want (head: +19 and -19; tail: between +5 and -5), but what I found is the membrane atoms are all shift up after 25ps MD, even though the center of the entire system (membrane+water+ion) is 0, 0, 0, but the center of the membrane shift to like 0, 0, 2. when I looked at the structure in VMD, it is obvious that there are thinner layer of water on the top of the membrane, and a much thicker layer of water on the bottom. I also found the bigger force constant I used, the more the center will shift up. if I remove the colvar part from my input file, then there is no prolem.
>>
>> here is my ColvarsConfig,
>>
>> ##Lipid Head###
>>
>> Colvarstrajfrequency 100
>> Colvarsrestartfrequency 100
>>
>> colvar {
>> name head_POPC
>> distanceZ {
>> ref {
>> dummyAtom ( 0.000, 0.000, 0.000 )
>> }
>> main {
>> atomsFile head_POPC_main.ref # head atoms #
>> atomsCol B
>> atomsColValue 1.0
>> }
>> }
>> }
>> harmonic {
>> colvars head_POPC
>> centers 19 # or wherever the head group should be (15, 18, 17...) #
>> forceConstant 5
>> }
>>
>>
>> ###lipid tail###
>>
>> colvar {
>> name tail
>> width 0.1
>> lowerboundary -10.0
>> upperboundary 10.0
>> lowerWall -5.0
>> upperWall 5.0
>> lowerWallConstant 5
>> upperWallConstant 5
>> distanceZ {
>> main {
>> atomsFile tail_main.ref
>> atomsCol B
>> atomsColValue 1.0
>> }
>> ref {
>> dummyAtom ( 0.000, 0.000, 0.000 )
>> }
>> axis (0.0, 0.0, 1.0)
>> }
>> }
>>
>> Can anyone give me some suggestions here, I am really confused. Thanks a lot!
>>
>>
>> Emilia
>>
>>
>>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:23 CST