GROMACS CgenFF Overriding UB parameters warnnings?

More Yiran Qu's questions See All

Gromacs force field and water model recommended for protein hydrophobic study?

Dear All, I received a comment from reviewer about asking me selection of force field and water model. I choose OPLS-AAL and 3-point water model. They mentioned the combination of OPLS-AAL and SPC...

13 February 2021 1,364 3 View

Gromacs: dssp issue?

Hi, when I try to analyze protein secondary structures using gromacs gmx do_dssp command, it keeps telling me specifying dssp version. I realized I can only give integer number, so I try -ver 3....

08 September 2019 2,387 11 View

Energy minimization in LAMMPS using NVT ?

How do I do energy minimization in lammps with NVT ensemble ? I am using the following command and it does not seem to work. It stops at extremely high energy and gives me the error zero search...

01 March 2021 2,294 3 View

How can I integrate a routing protocol in a tiny device (e.g. Raspberry Pi)?

Hi Community, I'm facing the issue of integration/compiling a new routing protocol in a WSN simulator. The final goal is to successfully add, configure this routing protocol in hardware devices...

01 March 2021 9,332 6 View

How can I edit suggested publications?

Hi there! I regularly receive suggestion about papers and authors that are totally out of my area. Does anybody know how I can fix this? Thank you!

01 March 2021 9,574 4 View

How to improve and implement WBAN MAC and Radio modules under Castalia 3.2 ?

Hello researchers, Hello Castalia3.2 researchers I am a beginner with Castalia, I work on optimization of RFID systems used in wireless body networks. I simulated a WBAN with 10 nodes and one...

28 February 2021 400 1 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

D2D implementation in Matlab in Vienna LTE software?

Hi Hope you are well. Can you please share your code for D2D implementation in Matlab. I want to implement D2D in Matlab based Vienna simulator and struggling to deploy D2D. Thanks

24 February 2021 9,378 3 View

What software programs can directly simulate Additive Manufacturing Directed Energy Deposition (DED)?

I understand there are a lot of software programs that can simulate DED by going through specific modeling, simulation, and commands. For me, that was time consuming and results were not accurate....

24 February 2021 4,428 3 View

Is it possible to set a breakpoint at a specific DYNAMIC instruction using the GNU Debugger (GDB)?

Using GDB, it is straightforward to debug and monitor a target program by setting a break-point at a specific instruction, since the instruction addresses are known. However, we have two...

24 February 2021 1,598 2 View

Langevin Dynamics in shear flow?

Hi, We are trying to simulate particles with Langevin dynamics in a shear flow by Lees-Edwards boundary conditions in MD simulations. It seems thermal forces and shear flow do not go hand in...

23 February 2021 1,761 1 View

Can you perform the Murexide test on samples fixed in Formalin?

I have a fixed sample and would like to use the murexide reaction to test for uric acid composition. I no longer have fresh samples

22 February 2021 1,328 1 View

Justin Lemkul

The parameters already exist in ffbonded.itp because the CGenFF server version is older (4.0) than what we provide in the CHARMM36 port (4.1). Delete the lines in the .prm file that cause the parameter clash.

Yiran Qu

Hi, Justin!

For errors reminding, I delete the lines directly. How about the warnings? Do you suggest I could delete them directly as well?

Thanks for reply!@Justin

Yes, you need to deal with all of it. Angles can (in principle) be overridden, which is why it's a warning. Type 9 dihedrals are the sum of multiple terms, and is an error because when there are non-continuous blocks of parameters, that will produce undesired behavior.