Re: Reference file for the constraining force in Umbrella Sampling

From: Mert Gür (gurmert_at_gmail.com)
Date: Sat Mar 14 2009 - 07:10:35 CDT

Thanks a lot for your quick response it was very heplfull. Two more quick
question just to be sure:

I want to do a second steered molecular dynamic simulation starting from the
coordinates at the end of my constrained simulation, so that I can perform a
second constrained simulation at another position.
Shall I make a ref file from a frame at the end of my constrained simulation
trajectory to generate the SMDFile file?

Should my coordinate and structure files at the top of my second SMD
simulations configuration file be the pdb and psf files I just generate at
the very beginning of my first SMD simulation and used for my first SMD
simulation?

I attached my conf file in case you want to take a look.

Best,
Mert

On Fri, Mar 13, 2009 at 1:30 AM, Eric H. Lee <ericlee_at_ks.uiuc.edu> wrote:

> No, the restraint file uses the coordinates within that pdb file as
> equilibrium positions from which to apply the constraint - you will have to
> make a new ref file from a frame at the end of your smd trajectory once the
> protein is where you want it to be. You might as well use this same file
> for the spring constant file (kfile) putting the spring constants in the
> occupancy column.
>
> -Eric
>
> On Mar 12, 2009, at 6:02 PM, Mert Gür wrote:
>
> Hi everyone,
> What I am trying to is:
> I first move my protein(prot.psf,prot.pdb) along my reaction coordinates
> with steered molecular dynamics. Lets say its stops at a final position.
> I want to apply constraining potential at that point. What should I take to
> generate my consref and conskfile files . Should it be the same coordinates
> with
>
> prot.pdb which I used in SMD as coordinates prot.pdb
>
> or should I use the final restartcoordinates of my SMD simulation. Or does
> it even not make any difference which coordinates I use for my consref and
> conskfile files .
>
>
> if {$cons == 1} {
>
> constraints on
>
> consexp 2
>
> consref $ref_res
>
> conskfile $ref_res
>
> conskcol O
>
> selectConstraints on
>
> selectConstrX off
>
> selectConstrY off
>
> selectConstrZ on
>
> } else {
>
>
> Eric H. Lee
>
> Medical Scholars Program
>
> Theoretical and Computational Biophysics Group, UIUC
>
> ericlee_at_ks.uiuc.edu
>
>


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