RE: Included Topology (.itp) in gromacs to parameter file for NAMD

From: Vermaas, Joshua (
Date: Wed Jul 11 2018 - 12:16:11 CDT

Hi Ivan,

This is a NAMD error at runtime. What does the rest of the log look like, and what sort of hardware are you running NAMD on?


On 2018-07-11 03:01:08-06:00 Ivan wrote:

Hello again Josh, I was very thankfull when I read your fast response. It's taken me a while to investigate all the options and advance the project. Now I'm facing new problems and I didn't found any good information among all mailing list and google. I've noticed there are lots of questions about this, but unanswered.
When I run the simulation, this error appears:
Charm++ fatal error:
unexpected call to exit by user program. Must use CkExit, not exit!
I haven't found any exit! on my scripts, any idea why could this be happening?
Best regards,

On 3 July 2018 at 20:58, Vermaas, Joshua <<>> wrote:
Hi Ivan,

Ick. Based on what is described in the GROMACS documentation, where you effectively "make your own" dihedral potential, I don't recall a similar feature existing in NAMD. If your potentials happen to be sinusoidal, you can use the "extraBonds" interface to define them yourself (<> or write a proper CHARMM-style parameter file for your inputs. Is there a particular reason you don't want to use GROMACS? Or failing that LAMMPS, which I recall also has a similar feature?


On 2018-07-03 12:44:14-06:00 Ivan wrote:

Josh, thank you very much for your rapid and nice answer. The tabulated table .xgv is a parameter to mdrun. Any advice or idea would be highly appreciated.
Again, thank you very much for replying.

On 3 July 2018 at 18:51, Vermaas, Joshua <<>> wrote:
Hi Ivan,

How is this fed into GROMACS? Is the .xvg fed in during the generation of the .top file, or is it a parameter to mdrun? NAMD should be able to read in a GROMACS .top file (see<> if it is the first option, with the caveat that NAMD doesn't parse "#include" statements in a .top file, but not if it is the second.


On 2018-07-03 02:46:48-06:00<> wrote:

Thank you very much for all the work you do and keeping the NAMD project alive.
I've recently seen an article about a customized force field for GROMACS with an .itp extension and a .xvg tabulated table for the dihedral interactions. I would like to convert that to use it on NAMD and continue to make accurate simulations using NAMD, so it has to have AMBER or CHARMM format I guess.
I've searched the internet and on this site I found this:
"... the Gromacs force field uses a different type of function
(for proper and improper dihedrals) than the Charmm force field. Gromacs
appears to use harmonic and periodic functions while Charmm uses modified
Fourier series. ">
How can I solve this? Any idea? Is this even possible to do?
Thank you in advance,

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