[gmx-users] gromacs.org_gmx-users Digest, Vol 161, Issue 42

[Yanke Peng]

Hi, Justin thanks again for your reply!
1. The 352 water molecules in a .gro file was actually gotten.  I have
checked it by viewing the .gro file and by the VMD and Avogrado software.
2. Could the failure be caused by the out-of-box hydrogen atoms? (Some of H
atoms are out of the definition box boundary)
3. The force field and water model I used are AMBER99 and TIP3P.

> ------------------------------
>
> Message: 5
> Date: Mon, 11 Sep 2017 07:58:28 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Crystallization of NaCl saturated aqueous
>         solution under high temperature of low pressure.
>
> On 9/11/17 1:53 AM, Yanke Peng wrote:
> > Hi, Justin, Thanks very much for your advice.
> > I think I should try a low concentration NaCl to verify if the system has
> > the chance to be energy minimizated.
> >
> > Here are the exact commands that I used.
> > 1. solution definition
> > #water box and topology file generation
> > gmx solvate -box 2.48 2.48 2.56 -o water.gro -maxsol 352
>
> Does this actually fill the box appropriately, and do you actually get
> all 352 waters?
>
> > gmx pdb2gmx -f water.gro -p water.top
> > #get water.tpr
> > gmx grompp -f water.mdp -c water.gro -p water.top -o water.tpr
> >    (#content of water.mdp file: integrator=steep)
> > #get solution.gro
> > gmx genion -s water.tpr -np 32 -pname NA -nn 32 -nname CL -o solution.gro
> > -p water.top
> >   (after 32Na+ and 5Cl+ was replaced. The fatal error shows "No more
> > replaceable solvent")
>
> This should be your first indication of a problem.? If you actually have
> 352 waters, there should be no issue adding 64 ions.? Visualize the
> structures at each step, and verify the contents of the topology.? If
> you ask for 32 of each ion, you should get it.? If you don't, stop and
> re-evaluate what you have done.
>
> -Justin
> ******************************************************
>



-- 
Yanke Peng
Visiting Ph. D Candidate
Department of Mechanical Engineering, University of Minnesota