Re: SMD atoms are not moving in accordance with steering parameters!

From: Peter Freddolino (
Date: Fri Jun 22 2007 - 07:59:14 CDT

Hi Gungor,
have you checked your SMD output to make sure that a force of the
appropriate magnitude and direction is being applied during those
pullings that you think are incorrect? Also, are you updating your
SMDFile between pulling to make sure the appropriate reference
coordinates are used? What value is being used for the SMD spring constant?

Gungor Ozer wrote:
> Hi Peter,
> Total simulation time is 0.1ns. What I need to achieve is a circular
> path of the steered residue. So, I am doing 10 different SMD runs each
> having 0.01ns simulation time (10 x 0.01ns = 0.1ns) and each starting
> from the end of the previous.
> Therefore, I am changing the direction vectors at each step in order
> to satisfy a circular path. SMDVel is around 0.000335.
> I am actually having some good approximate pullings for several of
> these steps. However, in at least three of them it is going somewhere
> completely irrelevant to my pulling direction.
> Let me give you some example (this is the final step, 0.09ns -> 0.1ns):
> Let's say I have two fixed residues A and B, and another one C being
> steered.
> B-C distance should be around 14.4A and A-B-C angle should be around
> 144 at the end of the simulation. What I keep getting is that B-C =
> 20A and A-B-C = 108.
> As you can see, residue C is travelling to a completely different
> location than I wanted it to move.
> Hope that would help you visualize my problem. Thanks for your
> interest and inquiry...
> -gungor
> On 6/21/07, Peter Freddolino <> wrote:
>> Hi Gungor,
>> could you please elaborate on this behavior a bit? How exactly did the
>> pulled residue move? How long was your simulation? And did the SMD lines
>> of the log file indicate pulling in the appropriate direction?
>> Peter
>> Gungor Ozer wrote:
>> > Hello all,
>> >
>> > I have been trying to run a Steered MD simulation on a small peptide.
>> > What I've been doing is basically pulling a whole residue at a
>> > realtively appropriate velocity (10^-4 orders of magnitude of
>> > A/timestep) in a box full of TIP3 water molecules at 500K. The
>> > aminoacid is not a part of a beta strand or an alpha helix and its
>> > only non-bonded interactions are those with waters.
>> >
>> > The problem I am facing is simply that my steered residue was not
>> > moving along the direction vector and velocity I have been assigning.
>> >
>> > Does anybody know what I might be doing wrong? Or, has anybody
>> > experienced similar problems? And finally, do you have any potential
>> > explanation (or solution) to this issue?
>> >
>> > Thank you all in advance...
>> >

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