From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Wed Oct 04 2017 - 11:48:43 CDT
Thank for replying!
I have put both colvars into one *.in file and I can see that the output
shows both colvars in one output file. I am not sure how WHAM interprets
the output file though, since it contains additional column of data.
>>Keep in mind that if you put restraints that affect the ion conduction
pathway, you have to question yourself whether you are changing the
resulting PMF, which has to assume a minimum free energy pathway.
During regular equilibration (not US runs) I do observe interaction between
ions and this particular site, however ions don't stay there long, they
proceed almost immediately further down the channel towards stronger sites
inside. I think that because the ion is confined to move in the small
window it shifts towards this residue in this particular window (and a
couple of adjacent windows) and does not leave for the rest of the run
because interaction with the residue is too strong. Does it make sense?
I wonder if increasing the force constant in the input file would affect
this? I use 2.5 kcal/mol*A with width 1.0, and it works well inside the
channel. Is it reasonable to use a bigger force constant (say, 5 or
7kcal/mol*A) at the entrance or is it better to have the same force
constant for each window during PMF simulations?
On Tue, Oct 3, 2017 at 4:16 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> You can split configuration for different variables in multiple files, and
> load them using "cv configfile" or even put them as strings (between double
> quotes) in the NAMD main script and load them through "cv config".
> Keep in mind that if you put restraints that affect the ion conduction
> pathway, you have to question yourself whether you are changing the
> resulting PMF, which has to assume a minimum free energy pathway.
> On Tue, Oct 3, 2017 at 1:45 PM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>> Hi all,
>> in my current umbrella sampling simulations for ion permeation through
>> the channel I see ion shifting off the center line (where it supposed to be
>> located) near the entrance or exit of the pore (no shift in the windows
>> inside the pore). It seems to move to the nearest strong residue and stay
>> there throughout simulation without returning back to the specified centre.
>> The ion can move 2-3 A to the side over the first 0.5-1 ns and linger there
>> for the rest of the simulation. I use distance colvar for this simulation.
>> I would expect that for umbrella sampling the ion should not shift that
>> far from a specified location (and I haven't seen this in my previous US
>> simulations on a similar system). What would be the reason for this to
>> happen in US simulations?
>> I want to try using distanceXY colvar to restrain this movement. Is is
>> applicable in this case, in addition to distance colvar (i.e., not
>> distanceZ, but distance)? Do I have to have a separate input file for
>> distanceXY colvar or can I add it into the same *.in file as I have for
>> distance colvar?
>> Thanks in advance, I appreciate your advice.
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
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