Soroush Ziaei

7 Questions 12 Answers 0 Followers

Questions related from Soroush Ziaei

Is anyone else investigating the formation of a two-phase system between a carbohydrate and a solvent?

Dear Experts, I am currently conducting a Molecular Dynamics (MD) simulation using the NAMD package to observe the formation of a two-phase system between glucose, acetonitrile, and water. To...

27 May 2024 5,779 2 View

How to implement a µVT ensemble in molecular simulation software?

Hi experts, I heard we can use Grand Canonical Monte Carlo (GCMC) or a combination of other ensembles and techniques like a third-party plugin or script by modifying the source code. Also, maybe...

12 February 2024 2,614 6 View

Hi NAMD users, I have an error that I described below... please tell me what should I do?

recently, I encountered an error at the beginning of the simulation, which related to Atom 3662, please let me know the solution of this error: FATAL ERROR: Atom 3662 has bad hydrogen group size. ...

01 May 2019 8,476 2 View

Hi, i want to know how can i detect which atom should be -1 in fep file in order to obtain correct value for delta<g>?

or please describe some method to generate topology file for a unique structure, such as topology file that exist in tutorial (zero.top). meanwhile, is there a way to generate top.file for a...

27 October 2018 8,139 2 View

Hi, in order to calculation of free enrgy perturbation i have a protein structure file and i want to generate topology file from <psf> , how to do it?

is there a unique server to do it?

22 October 2018 6,766 0 View

Hi all, does anybody know about calculation of solvation free energy?

i tried on charmm-gui site but an error appears, what should i do? is there another way to calculate that?

28 February 2018 9,932 5 View

Hi all, does anybody have charmm program?

if someone have this software, I appreciate the one who send it.

12 February 2018 630 6 View