[gmx-users] position restrain dynamics error

Dear Sir, I am succesfully run molecules upto energy minimization, in case of position restrain md step , i have following, could you help to overcome the A charge group moved too far between two domain decomposition steps. Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviati

[gmx-users] reg minimization problem

Dear sir, i have running new molecules add in standard protein that new is morin molecules unfortunetly 102 error occur which is no defualt angle found , etc. i overcome this problem but one more new appear which is shown below could you help me to overcome these following errror 26 atoms ar

[gmx-users] REG: grompp comment

Dear sir, i have successfully created .gro file after neccessary correction made in .rtp file. In the grompp_d comment, i am facing following errror. could how can i rectify this error. my comment is ./grompp_d -f em.mdp -c abnic2.gro -p abnic.top -o abnic2.tpr WARNING 1 [file em.mdp,

[gmx-users] REGARDING DOUBT

dear sir, i have give input that is* ./pdb2gmx_d -f activesite16-22.pdb -water tip3p -ignh* but i face some* errror like There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb fi*le. i have m

[gmx-users] (no subject)

how to assign charge and charge group number when new residue as being added to the existing amino acid rtp file -- 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/Search

[gmx-users] regarding missing atom

dear sir, i was doing gromacs when i run pdb2gmmx i got following error that is some atom missing -- 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/Search before