simtk.org

Hi Peter,

I met with this problem when I tried to implement a position dependent Hydrogen Bonding term in openmm. However, I met with the problem of "unknown particle res_i". I don't have this problem when I access tabulated functions in other custom forces before. Is hydrogen bonding term different from other custom forces?

Many thanks in advance.

Sincerely,

Here is the code:

def beta_term_1(self, k_beta = 0.25*4.184):
print("new beta_1 term ON");
r_ON = .298
sigma_NO = .068
r_OH = .206
sigma_HO = .076
lambda_1 = np.zeros((self.nres, self.nres))
for i in range(self.nres):
for j in range(self.nres):
lambda_1[j] = self.get_lambda_by_index(i, j, 0);
theta_ij = f"exp(-(r_Oi_Nj-{r_ON})^2/(2*{sigma_NO}^2)-(r_Oi_Hj-{r_OH})^2/(2*{sigma_HO}^2))"
beta_string_1 = f"-k_beta*lambda_1(res_i,res_j)*theta_ij;theta_ij={theta_ij};r_Oi_Nj=distance(d1,a1);r_Oi_Hj=distance(d1,a2);"
beta_1 = CustomHbondForce(beta_string_1);
beta_1.addGlobalParameter("k_beta", k_beta)
beta_1.addPerDonorParameter("res_i");
beta_1.addPerAcceptorParameter("res_j");
beta_1.addTabulatedFunction("lambda_1", Discrete2DFunction(self.nres, self.nres, lambda_1.T.flatten()))
print(lambda_1)
for i in range(2):
if self.o!= -1:
beta_1.addDonor(self.o, -1, -1, );
if self.n!=-1 and self.h!=-1:
beta_1.addAcceptor(self.n, self.h, -1, )
beta_1.setCutoffDistance(1.0);
beta_1.setForceGroup(23)
return beta_1

Thanks! I just pushed a fix for the problem: https://github.com/pandegroup/openmm/pull/2232. I'll try to get it merged shortly.

Thanks a lot! I have noticed the changes, but could you tell me how to update the openmm suite (maybe through conda) with the most updated changes?

Sincerely,
Mingchen

You can install the latest nightly build with this command:

Hello,
I met with further problem when I updated my openmm using the above command: conda install -c omnia-dev openmm

python -m simtk.testInstallation
/Users/mingchenchen/anaconda2/envs/py36/bin/python: Error while finding module specification for 'simtk.testInstallation' (ModuleNotFoundError: No module named 'simtk')

It seems that simtk will not be available then. Any solutions?

Thanks and Best,
Mingchen

That means it didn't get installed correctly. Take a look in your site-packages directory. That should be something along the lines of /Users/mingchenchen/anaconda2/envs/py36/lib/python3.6/site-packages. Is the simtk directory there? If so, what does it contain?

Hello,

simtk is not there after installing the dev version. However, previously simtk was under that folder.

What does that mean? Do I need to install differently?

Thanks and Merry Xmas,
Mingchen

That means that somehow it didn't get installed correctly. I'd try again.

Thanks a lot for your help!

Enjoy the New Year.
Mingchen

Hello,

I am afraid this problem of installing DEV version has not been solved. I would very much appreciate your help to look into my issue.

Thanks and best,
Mingchen