From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Sep 12 2011 - 10:08:47 CDT
Hi Emilia,
t is difficult to restrain the water layer, and in general it is not
useful. If you want to keep water in a certain range, you'll have to
restrain *every molecule* individually, not just the group as a whole.
But why restrain water in the first place?
Jerome
On 12 September 2011 16:53, Ling Wu <emilia.l.wu_at_gmail.com> wrote:
> 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
>>>
>>>
>>>
>
>
>
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