faranak1991

@peastman Thanks for your reply. I am using the same force field and setting. To clarify, my question is whether OpenMM will begin the simulation using the last density and...

@aizvorski Thank you for the response. From what I understand, Interchange is not capable of converting Lammps data to OpenMM, but it does support the reverse direction, converting OpenMM to...

I am trying to compute the density of the attached pdb file using the following commands. However, the outcome I received seems remarkably different from the actual density, which is...

Thanks for your recommendation, I will check that.

@WangXinyan940 . I appreciate your answer. I've recently visited the "pymbar" page, but I'm still somewhat puzzled about how MBAR handles the new force field parameters that haven't undergone any...

Dear @KuangYu, I appreciate your thorough response. Upon reviewing your DMFF paper, I've noticed that in the workflow depicted in Figure 2, the modified parameters are returned to MBAR as...

@KuangYu. To clarify, when you mention "resample," you are referring to conducting a MD simulation using the updated parameters. This simulation is necessary to generate the reduced potential energy required...

Thank you for your reply @lilyminium. The error was resolved by installing the specific version of Pint. Additionally, I have provided the list of packages installed in the Conda environment...

Thanks @mattwthompson . I see that certain properties have already been specified as follows. Is there any possibility to include transport properties such as viscosity in the existing set? Also,...

conda list : # Name Version Build Channel alabaster 0.7.13 pyhd8ed1ab_0 conda-forge ambertools 23.3 py311ha883923_1 conda-forge amberutils 21.0 pypi_0 pypi anyio 3.7.1 pyhd8ed1ab_0 conda-forge appnope 0.1.3 pyhd8ed1ab_0 conda-forge argon2-cffi 21.3.0...