From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Aug 28 2012 - 12:17:20 CDT
in terms of them being different, are you certain the frames match? That
is, does your colvarsTrajFrequency match your DCD frequency? Are the atoms
you are choosing the same? In VMD if you are talking about the atoms you
mention in your NAMD script you want to use 'serial' rather than 'index' I
believe.
not sure beyond that what would cause a difference.
~Aron
On Mon, Aug 27, 2012 at 6:54 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
> Hello Sudipta:
>
> 1) Any keyword that you don't know the meaning of, don't include it: leave
> the default values for that.
> 2) It would help others to help you if you reported the exact numbers,
> when you say that the values reported by NAMD and VMD are "significantly
> different".
> 3) If you want to restrain the distance variable around one value, use the
> value with PBC.
> 4) Decide whether you want to restrain around one value, or within an
> interval (you actually wrote the latter).
> 5) Increase the force constants until you are satisfied, or the simulation
> blows up in pieces.
>
> Giacomo
>
> On Mon, Aug 27, 2012 at 6:41 PM, sudipta <sudipta.mml_at_gmail.com> wrote:
>
>> Hi All,
>>
>> I need to perform a restrained simulation of protein molecule. In this
>> regard, I need your help. To perform that simulation, I have chosen two
>> groups of protein atoms and COM distance between these two groups of atoms
>> is the collective variable. The input parameters are given below,
>>
>> colvarsTrajFrequency 100
>> colvarsRestartFrequency 100
>>
>> colvar {
>> name comdis
>>
>> width 5.0
>>
>> lowerboundary 0
>> upperboundary 133.0
>>
>> lowerWallConstant 0.1
>> upperWallConstant 0.2
>>
>> outputAppliedForce on
>> outputVelocity on
>> outputSystemForce on
>>
>> distance {
>>
>> group1 {
>> atomnumbers {3442 4835}
>> }
>> group2 {
>> atomnumbers {4137 4140}
>> }
>> }
>> }
>>
>> I have manually calculated the COM distance between these two group of
>> atoms and the value is significantly differ with the namd output which is
>> written in .colvars.traj file. The two values are 132.33 (35.3 with PBC) A
>> and ~60 A. My aim is to sample the protein molecule in such a manner where
>> the distance between those two defined group of atoms of the protein
>> molecule fluctuate around 132.33 A with some standard deviation (say 5 A).
>> So how to reach my aim. Any suggestion will be highly appreciated.
>>
>> Thanks in advance
>> Sudipta
>>
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:26 CST