[gmx-users] Density of the box

Thank you Tsjerk! Actually I was not using any dummy atoms or united atoms in this case. I was using a pdb file with just water atoms (1BP2). Kindly excuse me I was not recieving any replys to my mail id ka...@rishi.serc.iisc.ernet.in. -- gmx-users mailing listgmx-users@gromacs.org http://li

Re: [gmx-users] Density of the box

Hi, editconf needs to take the masses from a database file if not fed with a run input file. It will probably miss out on some types of atoms or get the masses wrong, especially with united atoms and/or dummies. Probably the density would be correct giving a .tpr file for input. Cheers, Tsjerk

Re: [gmx-users] Density of the box

Sir, I am using Gromacs 4.0.7 version. Does this problem exits in other older or newer versions? what is the density of water that spc216 adds? If it is a fixed density, then i encountered a problem - I tried using 1 water molecule as a system (instead of protein), in a cubic box with 0.8nm

Re: [gmx-users] Density of the box

On 10/01/2011 7:59 PM, ka...@rishi.serc.iisc.ernet.in wrote: Dear Gromacs users, I was trying to run a simulation using a protein of 123 aa long and wanted to adjust the density to 993.04g/l so with the following command I ran the editconf: editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -den

[gmx-users] Density of the box

Dear Gromacs users, I was trying to run a simulation using a protein of 123 aa long and wanted to adjust the density to 993.04g/l so with the following command I ran the editconf: editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -density 997.0479 Its output was as follows: