[gmx-users] Generation of 1-4 nonbonded parameters for CHARMMff

- I apologize for resubmitting the question as my previous mail was not properly sent. Dear gromacs users, I'm trying to build a new topology and a parameter file of a small organic molecule. My strategy is to use CGENFF(and paramchem.org) to generate CHARMM topolog

[gmx-users] Multiplicity of a dihedral

Hello, How is the multiplicity of a dihedral determined? I know that it is related to the number of minima, but then how could we determine the number of minima? Is it with chemical intuition or with QM calculations? My molecule has several rings, which makes it not possible to calculate energ

[gmx-users] Adding His tag to N-ter of a protein

minus, but failed as the chain is no longer recognized as a protein after the modification. I would be grateful if anyone could give me a clue on this. Many thanks in advance. Sincerely, Jong Wha Lee -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

[gmx-users] Is vacuum simulation NVT?

Dear Gromacs users, Is a vacuum md simulation an NVT simulaton? As the pressure and energy are not fixed, I think that the only option left is NVT. But without pbc, the volume would not have been defined. Can it still be called NVT? Thanks, Jong Wha -- gmx-users mailing listgmx-us

[gmx-users] Re: Re: Is vacuum simulation NVT?

Thank you very much Justin, and thank you very much Michael. Your replies were of a great help. Jong Wha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searc

[gmx-users] Lennard-Jones potential for protons

Dear Gromacs Users, Hi, I'm trying to simulate a system with a free proton included. However, I wasn't able to find Lennard-Jones parameters for free protons in charmm, amber, and opls ff. On the other hand, there are parameters for other cations such as Na, K, etc. Is there any reason why par

[gmx-users] Re: Re: Lennard-Jones potential for protons

Thank you Mark and Vitaly. I understand that simulation of protons in the solution phase is unphysical. Though I haven't mentioned beforehand, I'm actually trying to simulate noncovalent interaction between a proton and a carbonyl oxygen in the gas phase. Could you give me any ideas how I may s

[gmx-users] Calculation of binding enthalpy in vacuum

Dear Gromacs users, I’m trying to calculate the binding enthalpy of a host molecule with a guest molecule in vacuum. I cannot perform QM calculations because some systems I’m studying are too large. I know that free energy calculations are possible with Gromacs, but they require some cautio

[gmx-users] Re: Re: Calculation of binding enthalpy in vacuum

Dear Vitaly, Thank you for your suggestion. I have also tried calculating interaction energies by specifying energygrps in .mdp file, but calculated energies deviate greatly from QM calculated energies and experimental results. I suspect that the structure of each component in complex diffe

[gmx-users] Re: Re: Re: Calculation of binding enthalpy in

Dear Vitaly, Thank you very much for your reply. I originally asked the question because I wasn't sure my values were from correct procedures. Now I see how I could properly calculate binding energies with MM. John Lee > Dear Vitaly, > > > > Thank you for your suggestion. > >