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 <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 > ****************************************************** > -- Yanke Peng Visiting Ph. D Candidate Department of Mechanical Engineering, University of Minnesota -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
