On 9/11/17 1:05 PM, Yanke Peng wrote:
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)
No. Replacements are made based on O atoms, and periodicity is handled.
3. The force field and water model I used are AMBER99 and TIP3P.
OK, this shouldn't matter.
-Justin
------------------------------
Message: 5
Date: Mon, 11 Sep 2017 07:58:28 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@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
******************************************************
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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