Hi dear all,

I’m trying to calculate pmf of two particles as a function of distance using fix smd command. I fixed r0 to zero according to Mr.Kohlmeyer’s suggestion mentioned in the related mails. So I’ve used this command :

fix pmf g1 smd cvel 10 15e-5 couple g2 0 0 1 0.0

.

manual says that the last column of the array computed by this fix is “the

accumulated PMF (the sum of pulling forces times displacement)”

but I don’t get what i expect as the PMF increases or decreases monotonously with distance increase or decrease.

what is wrong with my run input?

Or is this “accumulated PMF” not the famous potential of mean force? I read a Mr.Kohlmeyer’s answers saying : "

```
here is what is accumulated into pmf:
pmf += (fx*xn + fy*yn + fz*zn) * v_smd * update->dt;
so it is the integral over time of the force projected
on the pulling/pushing direction. this is done in every
step so a sophisticated numerical integration is not needed."
.
```

```
so as I understand there's no difference but the results are not acceptable.
```

And another question: using this fix distances less than r(minimum) are not sampled. I have been able to do this using fix spring command and then calculated PMF using WHAM method. but with fix smd there’s no sampling in those distances.

how can I sample distances less than r(minimum) with fix smd?

thank you.

Hi dear all,

I'm trying to calculate pmf of two particles as a function of distance using

fix smd command. I fixed r0 to zero according to Mr.Kohlmeyer's suggestion

mentioned in the related mails. So I've used this command :

fix pmf g1 smd cvel 10 15e-5 couple g2 0 0 1 0.0

.

manual says that the last column of the array computed by this fix is "the

accumulated PMF (the sum of pulling forces times displacement)"

but I don't get what i expect as the PMF increases or decreases monotonously

with distance increase or decrease.

what is wrong with my run input?

Or is this "accumulated PMF" not the famous potential of mean force? I read

a Mr.Kohlmeyer's answers saying : "

here is what is accumulated into pmf:

pmf += (fx*xn + fy*yn + fz*zn) * v_smd * update->dt;

so it is the integral over time of the force projected

on the pulling/pushing direction. this is done in every

step so a sophisticated numerical integration is not needed."

.

so as I understand there's no difference but the results are not acceptable.

impossible to comment on without seeing a usable input example.

And another question: using this fix distances less than r(minimum) are not

sampled. I have been able to do this using fix spring command and then

calculated PMF using WHAM method. but with fix smd there's no sampling in

those distances.

how can I sample distances less than r(minimum) with fix smd?

what is "r(minimum)"?

axel.

...oh, i forgot to add.

if you don't like the interface of fix smd, you can check out

the USER-COLVARS package. it uses the colvars library

that is also used in NAMD and can do steered MD (as well

as metadynamics, umbrella sample and ABF).

axel.

By r(minimum) I meant the distance in which the minimum of PMF occurs or the potential well. I am sorry for not clarifying what I meant.

And I read about NAMD and other methods but the problem about SMD seems not to be too complicated. The main problem now is that I cannot sample the system in distances less than r(minimum) due to high LJ repulsion forces.

I have set a primary distance (15 Angstrom) and it is reduced with a constant velocity. this distance as I monitored in the log file is the equilibrium distance of the spring implemented by the fix smd. Everything’s fine until the two particles reach a distance (4 Angstrom) and stay at it even when the equilibrium distance of the spring becomes less than 4. this seems to be the distance in which particles are in the potential well. But I need to sample distances less than this too.

I could perfectly sample this area too, with umbrella sampling using fix spring. But since that method needs a post processing procedure (WHAM) I prefer to use a more straightforward way like SMD.

thank you.

As I wrote before, provide an example input that reproduces your problem. Impossible to discuss otherwise since I cannot read minds.