how to not overwrite a modified file? (while producing coordinates for ABF/US windows)

From: Olya Kravchenko (
Date: Sat Aug 06 2016 - 07:18:56 CDT

Hi all,

I am trying to produce a trajectory for calculating PMF for an ion
channel. I am doing it the following way:

-position the ion in the beginning of the channel and equilibrate
-use the last frame of the dcd file, shift the starting position of
the ion by 2 A and equilibrate
-use the last frame of the previous simulation, shift the ion by 2A
and equilibrate

..and so on, for 15 frames, until the ion is in the end of the channel.

I only modify the position of the ion, and the protein is unchanged.

This way I am trying to get pdb files for 15 consecutive windows to
further use with US and possibly ABF calculations. Is this an
appropriate way to get a trajectory? (apart from SMD simulations)

The ion sinks into the channel faster and I have to return it (instead
of advancing it) to get the next consecutive window. F.e. window0
starts at z=136, and then I want window1 to be z1=134, window2 to be
z2=132, etc. The last frame of the window0 simulation show that ion
sinked to z=126, so I return it to z=134 for window1 simulation and
save coordinates in a w1.pdb to use in a configuration file for the
next equilibration.

But when I load a dcd file for each consecutive window, I see that in
the very first frame the position of the ion is already way further
down than in my input pdb file that I prepared after saving
coordinates from the previous run and shifting back the ion.

I am afraid I may be overwriting the modified file by the restart.coor
file from the previous run. Can that be the case or is there another

If I want to use new pdb (where the only thing that is modified is the
position of the ion) and leave the rest of the protein unchanged, and
continue simulation, how do I make sure that the newly modified
coordinates are used?

I'll appreciate your input.


P.S. Here is a part of my configuration file:

# equilibrate for 300 ps

structure final.psf
coordinates w3.pdb
outputName w3

set temperature 300

# Continuing a job from the restart files

if {1} {

set inputname w2

binCoordinates $inputname.restart.coor

binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use


extendedSystem $inputname.restart.xsc


firsttimestep 810000

Here final.psf is the original psf file for the whole structure that I
figured is not going to change throughout simulation as the only thing
I modify is the position of the detached ion.

w2, w3 are consecutive windows. w3 is created by saving last frame of
the w2 equilibration and shifting the ion.

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