[gmx-users] Minimization stops without reaching the requested precision Fmax < 1000

Dear Gromacs Users, I am trying to add the tethrahedral zinc atom dummy model into CHARMM36 force field in Gromacs. In my system, this dummy zinc interact with four Cystein residues (CYM). The parameters of the zinc are available in CHARMM format, which I used to use it in NAMD package. After

[gmx-users] Minimization stops without reaching the requested precision Fmax < 1000

Dear Gromacs Users, I am trying to add the tetrahedral zinc atom dummy model into CHARMM36 force field in Gromacs. In my system, this dummy zinc interact with four Cystein residues (CYM). The parameters of the zinc are available in CHARMM format, which I used to use it in NAMD package. After

[gmx-users] CHARMM36 in Gromacs :DNA terminus residues problem

Dear all, I am trying to do MD simulation on my protein-DNA system in *Gromacs* using *CHARMM36* force field (*2019 version*, downloaded from Mackerell web homepage). The DNA residue names start from DG5 ==> DC3 (in both DNA strand): Once I do *pdb2gmx* command, seems it does not correctly

[gmx-users] Constraints Error; In Using Tetrahedral Zinc Dummy Model

Dear Gromacs users, I am trying to simulate a zinc-finger protein in explicit water, *with CHARMM36 FF*. Unfortunately, I did not find any *tetrahedral zinc force* field in Gromacs and therefore I converted the tetrahedral dummy zinc model used in CHARMM27 FF to the format of Gromacs. The

Re: [gmx-users] -t option?

Hi Hadi, It is well explained in Gromacs tutorial, in the below: http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html "Note that we are now including the -t flag to include the checkpoint file from the *NVT* equilibration" Cheers, Mahdi On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad

[gmx-users] Constraints Error; In Using Tetrahedral Zinc Dummy Model

Dear Gromacs users, I am trying to simulate a zinc-finger protein in explicit water, *with CHARMM36 FF*. Unfortunately, I did not find any *tetrahedral zinc force* field in Gromacs and therefore I converted the tetrahedral dummy zinc model used in CHARMM27 FF to the format of Gromacs. The

Re: [gmx-users] How to parametrize a new molecule?

Hello Herbert, Not related to your question, but be careful if you are going to use CHARMM36 force field for DNA, as a recent study ( https://pubs.acs.org/doi/10.1021/acs.jpcb.9b09106) shows that this ff does not preserve DNA stability at a longer time scale, in case you are going to do so.