[gmx-users] non water solvation
jalemkul at vt.edu
Sat Jan 13 14:54:53 CET 2018
On 1/13/18 6:06 AM, mmahmoudig at razi.tums.ac.ir wrote:
> i want use from ethanol box instead of water, But I do not know what to
> write instead of spc in this command(gmx pdb2gmx -f 3HTB_clean.pdb -o
> 3HTB_processed.gro -ethanol spc)?
There is no such option. You don't need to specify any kind of water
model if you're not going to make use of it; the only purpose for that
argument/selection is for pdb2gmx to know which #include statement to
write in the .top file. In this case, you have none. You will need to
construct or obtain a pre-equilibrated box of ethanol for the purpose of
solvation as well as a topology that you will have to manually #include
in the system .top file.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users