[gmx-users] non water solvation

Justin Lemkul 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.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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