Dear Gromacs Users, First, I would like to thank Dr. Lemkul for reply.
My problem description is as follows: I am using CHARMM36 forcefield to equilibrate of AOT. when I add the mass of all atoms from topology, it gives me 444.5 which is correct but when I run the script editconf -c -f A.gro -o A.gro -density 1000 -bt cubic -box 5 -d 0.1 . It display incorrect value for mass of input. The mass of input should be 444.5 . The out come of above script is: Volume: 125 nm^3, corresponds to roughly 56200 electrons No velocities found system size : 0.215 0.234 0.157 (nm) diameter : 0.287 (nm) center : 2.500 2.500 2.500 (nm) box vectors : 5.000 5.000 5.000 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 125.00 (nm^3) WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Volume of input 125 (nm^3) Mass of input 967.25 (a.m.u.) Density of input 12.8493 (g/l) Scaling all box vectors by 0.234221 new system size : 0.050 0.055 0.037 shift : 1.914 1.914 1.914 (nm) new center : 2.500 2.500 2.500 (nm) new box vectors : 5.000 5.000 5.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 125.00(nm^3) Here we can see that mass of input is 967.25 which is far beyond the reality. this will cause error in density and all other mass dependent parameters. Please help me how do I come over to this error Thank you so much for you kind help Hari -- gmx-users mailing list gmx-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 posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
