From: simone bardwell (sbard79_at_gmail.com)
Date: Wed Feb 15 2012 - 15:59:20 CST
Thanks for this Giacomo and for the tips regarding searching the user list.
If I could ask you to clarify one further point, when you say 'If you need
two structures (start and end), you can either define two RMSDs, or use a
combination of the two values', do you mean at the start the RMSD is 0 as
it overlays with itself and then at the end the RMSD is, for example, 10?
Sorry if I've missed the point here.
On Wed, Feb 15, 2012 at 7:48 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
> Hello Simone, the RMSD is with respect to one structure. You provide this
> structure via e.g. a PDB file, define the atoms to be fitted onto it, and
> the RMSD will be computed at every time step, on the same atoms. If you
> need two structures (start and end), you can either define two RMSDs, or
> use a combination of the two values.
>
> Searching the mailing list archives a bit more may have provided this
> thread from less than two weeks ago:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/15916.html
> where each of the answers can certainly help you.
>
> The message referred to ABF, but the difference with metadynamics is just
> using "metadynamics" instead of "abf". My general advice is, search for
> answers and/or example regarding a specific variable, because most of the
> times you can use on it any method you want. So searching for
> "metadynamics", "abf" or any other method will only narrow down your
> results.
>
> There is an example of input file, right in the relevant section of the
> NAMD user's guide:
>
> http://www.ks.uiuc.edu/Research/namd/2.8/ug/node54.html#SECTION000131300000000000000
> The example is to apply an harmonic restraint to a couple of distance
> variables.
>
> To adapt it to one of the 17 other types of variables, as I said try to
> search for that variable type first. Once you defined your variable,
> applying metadynamics or one of the other methods is pretty straightforward.
>
> Bests
> Giacomo
>
>
>
> On Wed, Feb 15, 2012 at 2:25 PM, simone bardwell <sbard79_at_gmail.com>wrote:
>
>> Hello
>>
>> I have a couple of questions regarding setting up
>> metadynamics calculations in NAMD. I have looked though the archive user
>> list but have not found a response to my questions.
>>
>> I would like to use RMSD as a CV for a metadynamics calculation. I would
>> like to be able to specify a start and end structure and then a set of
>> atoms to use to fit the structures together and then measure the rmsd of a
>> different region. I have read the Manual however am not sure if the region
>> being specified is for the fit and will also be the region to measure.
>>
>> My second question is whether anyone has any practical examples of RMSD
>> metadynamics input files they would be willing to share. I have searched
>> for tutorial examples for these types of calculations however with no
>> success. To be able to refer to an example would be really helpful.
>>
>> Kind regards,
>> Simone Bardwell
>>
>
>
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