Re: ABF atom selection

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue May 10 2011 - 09:59:08 CDT

Hi Parisa,

The difference in the results could just be a sampling accident -
these are stochastic simulations after all. There is not much else I
can say: I can just recommend that you inspect the trajectories in
VMD, and plot the time trajectories of the colvars, and see where the
behavior is different.

Best,
Jerome

On 10 May 2011 16:16, Parisa Akhski <Parisa.Akhshi_at_chem.queensu.ca> wrote:
> Hi Jerome,
>
> Thanks for your reply. I think it is better to use my own system and explain
> what I did so that I could realize what the problem is.
>
> I am running ABF simulation for Ammonium ion in the channel.
>
> I did the simulation for the same system in two different ways:
>
> 1. I define ammonium ion in the colvars as below:
>
> atomnumbers { 1 2 3 4 5}
>
> in which number 1 is the nitrogen atom and the rest are hydrogen atoms.
>
> 2. I define the ammonium ion in the colvars using only nitrogen atom:
>
> atomnumbers { 1 }
>
> in which 1 is the nitrogen atom number.
>
> In both cases I confine the ion movement in XY plane using "distanceXY".
>
> From what you said, I expect to get the same results for these systems.
> However, they are different and only the results of the second case, make
> sense for my system.
>
> I am wondering what is wrong with my definition and why the results are
> diffident?
>
> Thanks,
>
> Parisa
>
>
>
>
> -----Original Message-----
> From: heninj_at_gmail.com on behalf of Jérôme Hénin
> Sent: Sun 5/8/2011 12:41 PM
> To: Parisa Akhski
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: ABF atom selection
>
> Hi Parisa,
>
>> I am obtaining PMF profile using ABF method (NAMD 2.7 colvar). In
>> "hydration
>> free energy calculation for methane" in the tutorial, atom selection is
>> defined using atom numbers {1 2 3 4 5}. How this atom selection is
>> different
>> from defining only carbon atom number since carbon is the COM for this
>> molecule? I am assuming these two are the same.
>
> Almost, but not exactly. Using all atoms to define the group will
> collect more data, leading to faster convergence.
>
>> However, if I want to apply force to confine methane movement in XY plane
>> (using distance XY), this is not true any more. As I understood, in the
>> first case, force is applied to all atoms individually (not COM of these
>> atoms) whereas in the second case, force is only applied on the carbon
>> atom.
>
> That is not correct. For both coordinates, you can use either
> individual atoms or groups. If a force is "applied to a group" or
> "applied to the COM of a group", it means that it is distributed over
> all atoms in the group.
>
> Best wishes,
> Jerome
>
>

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