I am simulating a protein in a mixture of water and pyridine as a cosolvent I generated a box of water+py using packmol software
can someone tell me what exactly the steps I need to do solvate on GROMACS ? what command should I use and what input file necessary??
or if there is a tutorial on simulating a non aqueous system would really be helpful
thanks
It works pretty much like solvating with water. If you have the prepared mixed solvent box, most of the work is already done. Just use the mixed solvent as input for -cs.
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
hi Justin
thank you for replying I did as you suggested solvating my protein with the following command:
gmx solvate -cp protein_processed.gro -cs solvmix.pdb -o protein_solv.gro -p topol.top
it didn't make any errors but it seems to be stuck.. giving this warning:
Initialising inter-atomic distances...
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
it maybe that the input file I get from packmol is .pdb ~ and -cs requires .gro~ file??!
I don't know I'm new to gromacs if you have any farther suggestion I would really appreciate it
thanks again
The warning is basically irrelevant unless you have some bizarre elements in the solvent, e.g. "CA" will be interpreted as carbon and "HG" would be hydrogen. But if you've got some weird elements like calcium or mercury, the mass determination would be wrong. For 99.9999% of all systems, this is a non-issue. If there are no errors, your system is fine.
no I don't have any unusual atoms it is a common organic solvent
I'll try run it again
The Flowchart is in attached pic:
I'll answer any other question about Gromacs if any exists.
That flowchart is very outdated (.trr are not necessary for restarts, tpbconv and ngmx no longer exist, etc) and comes from old material in the GROMACS documentation. The new version is available at http://manual.gromacs.org/current/online/flow.html
so true dear Justin, it was presented as a procedure to start a research on codes.
by the way, thanks for your notice.
- Badges
- Science topic