Re: [AMBER] The long and winding STSM

From: Feng Pan <>
Date: Fri, 29 Jan 2021 15:37:48 -0500

Hello, Luis

From the figures you attached, generally it looks that it is OK even it
shows some strange behavior and maybe not converged.
Basically this is just a simple system to test string method is working but
cannot guarantee good results.
So any differences in parameters could lead to different results. Also the
force fields could matter. I am not sure if you used
a new force field? I remember I tested this example in an old force field
so this could be the reason.
Also you mentioned the two ends are not exactly the same as defined, and
this could be that the system is trying to find
some minima nearby as you assumed.


On Wed, Jan 20, 2021 at 10:57 AM Luis Simon <> wrote:

> Hi all,
> I have tried to run STSM calculation for obtaining the MFEP for the change
> of two backbone dihedral angles in a RNA hairpin, and I wonder if my
> results have some logic. I attach some pictures that hopefully will be
> shown in the mailing list, but just in case I will briefly describe them.
> I set up the calculation including 20 different images and 20 repeats. In
> each STSM calculation, equilibration run for 980 steps and release for 20
> steps. I set nstlim to 2000000 steps (dt=0.002, shake ON), although the
> calculations were not finished (however, the problems, or what I do
> identify as a problem, arose earlier than it stoped). I run it in both
> explicit solvent (around 18000 atoms) and GB implicit solvent (igb=1, 838
> atoms). For obtaining the initial geometries I set up steered calculations
> in which the restraints were moved from their values in one image to the
> value in the next.
> The first thing that surprised me was that the final images were not as
> close to the final point (epsilon=-180; theta=-30) as some other
> intermediate image (particularly, image number 16 seems very close to this
> final point. Why did STSM keep on “pushing” to more negative values of
> “theta”? Did I use a too large number of images?. Is it ok to obtain the
> PMF using umbrella-sampling with the first 16 images, ignoring the last 4
> wandering images.
> Another surprise was that the path, instead of “converging”, started to
> diverge towards less smooth lines as the number of iterations increased.
> That was particularly so in the case of the calculations with the explicit
> solvent. The implicit calculation seemed more consistent, but there are
> also some “artefacts”.
> I wonder if my settings were appropriate for this kind of simulations.
> Maybe the equilibration and(or release run for too low number of steps. Are
> 20 repeats/20 images a reasonable number for this kind of calculation?
> Thanks
> Luis
> PS-> The graphs show the torsion angles in degrees, but the calculations
> and covars were setup in radians. Also, I show the results for the
> “reparametrized centers”; “smooth” and “drift” centers look nearly the
> same.
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Feng Pan
Florida State University
Department of Statistics
AMBER mailing list
Received on Fri Jan 29 2021 - 13:00:02 PST
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