[gmx-users] How are the charges of the gromos96 forcefiel calculated ?

Dear users, I'm trying to find out how the atoms charges in the GROMOS96 force field were calculated but I've not been able to find out in the manual or in the paper I saw so far. I know that the force fields for MM have the atoms charges calculated by ab initio mathods but I wonder wit

[gmx-users] Triple bond

Dear users, We ve been trying unsucessfully to perform some MD simulations with some compounds containing triple bonds using GROMACS. Does someone know how to properly construct the topologies to this kind of bond for GROMACS ? With my best regards, Tanos C. C. Franca. -- gmx-u

[gmx-users] Error mesage

Dear gmx users, Does someone know how to deal with the error mesage bellow ? With my best regards, Tanos C. C. Franca. Program mdrun, VERSION 4.5.4 Source code file: domdec_con.c, line: 693 Fatal error: DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected via constraints from

[gmx-users] Error mesage

Dear gmx users, Does someone know how to deal with the error mesage bellow ? With my best regards, Tanos C. C. Franca. Program mdrun, VERSION 4.5.4 Source code file: domdec_con.c, line: 693 Fatal error: DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected via constraints from

[gmx-users] Charges

Dear gmx users, Does someone know in which file GROMACS store the information on the protein charge. I've seen that after running pdb2gmx or grompp the system charge is shown in the screen but we would like to know if this information is recorded in some file. With my best regards,

[gmx-users] Help with the heme group in forcefield gromos53a6

Dear users, We are trying to perform a MD simulation of a protein with a heme group using the gromos53a6 force field but, when trying to run grompp, we receive the error mesage: Program grompp, VERSION 4.0.3 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype FE

[gmx-users] file heme.rtp

Dear Gromacs users, I'm sure that the Gromos5A36 force field have topology to the heme group and would like to know how to proceed to perform a successfull MD simulation on a protein with this group. Should I just write the name of the heme topology file inside the protein.top file (jus

[gmx-users] How to include FE2+ in ions.itp ?

Dear GROMACS users, We're trying to perform a MD simulation of a system with a hematin group but realized that GROMACS does not have parameters for the ion FE2+. We tried to include the parametrs in the file ions.itp but did not suceed yet. Does anybody knows the right procedure to intr