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The problem of conflicting factors In MD simulation, in amber force field using 0.5 and 0.8333 scaling factors for 1-4 interaction van der waals and columbic interactions. However, in glycam based force field, these two scaling factors are set as 1.0 both.  In case we need to simulate a protein using amber force field and the LPS lipid using the glycam based force field in Gromacs, then there comes the problem. Because in Gromacs, the setting for these two factors (fugeJJ and fugeQQ) is written in the "[default]" field for the whole simulation system. Therefore, in order to generate 1-4 interactions for protein and LPS molecules, it will be incompatible. How to solve the problem? 1. Change protein force field to OPLS, using OPLS force field for LPS as well. Or choosing other force field. 2. Manually define the 1-4 interactions. But sadly only for vdw interactions. We could explicitly add parameters for 1-4 LJ interactions in the "pair" field. ...

Bugs? The newly released amber14sb made modifications for protein, DNA and RNA. This force field could be ported into gromacs as I already introduced previous. However, there are some small bugs in the improper dihedral angles of HID, HIE and HIP. So when generating tpr file, errors would be prompted. When run grompp -f npt.mdp -p topol.top -c protein.gro -o product.tpr -n index, errors occur: ERROR 1 [file topolff14sb_Protein_chain_B.itp, line 208041]:   No default Improper Dih. types The reason is that the parameters for some dihedral angles are missing. So we need to fix this. How to fix? Add the following two lines in the ffbonded.itp after the 730th lines: NA  CW  CC  CT       4      180.00     4.60240     2     ;;; HID force field added NA  CV  CC  CT       4      180.00     4.60240     2     ;;; HID force fie...

Amber force fields are popular for protein, DNA, RNA and lipid simulations. Recently updated amberff12, amberff14 and amberff15 were reported to perform better than amber99sb and amber99sb-ildn. Gromacs is a commonly used simulation software, which using OpenMM to enable GPU acceleration. Gromacs is fast and easy to use. A lot of people use amberff in Gromacs. So to use the newly release amberff12 and amber14sb in gromacs, we need to some work. Step 1. Install Gromacs 4.6.x or Gromacs 5.0.x or Gromacs 5.1.x Installation instructions could be find here: For 4.6.x http://www.gromacs.org/Documentation/Installation_Instructions_4.6 For 5.0.x and 5.1.x http://www.gromacs.org/Documentation/Installation_Instructions_5.0 Suppose you are user john, you installed a gromacs 4.6.7 in /home/john/applications/. After installation, you should source the GMXRC by: source  /home/john/applications/gromacs.4.6.7/GMXRC And add topology files to environments by: export GMXLIB=/home/joh...