[gmx-users] Crystallization of NaCl saturated aqueous solution under high temperature of low pressure.

Justin Lemkul jalemkul at vt.edu
Thu Sep 14 01:36:05 CEST 2017

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.


>> ------------------------------
>> 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
>> ******************************************************


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


More information about the gromacs.org_gmx-users mailing list