[gmx-users] Re: Hexamer problem/ high and low salt solutions.

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 7 15:33:19 CEST 2011

errabah fatima ezzahra wrote:
> Hi everybody
>  i did Again run the simulation for 2000ns and the proteins were just 
> moving every were , they were forming the two rimers but not for along 
> time like in the simulation with the 200ns and 20 ns.
> Justin : i did check the periodic boundary using VMD and it does not to 
> seem to be the case. thank you
> so I am thinking about running the simulation in diferrent solutions 
> like low salt , high salt and organic solvent ... I am new to gromacs 
> and i only used water to solvate the system and wondering if using 
> different pH solution and different salt concentration solution  is 
> something possible to do . i did some research and found out that you 
> can add ions like NA+ and CL_ but i was wondering if anybody does have 
> an idea of some solution that already have a pH known or solutions with 
> high salt concentaration that i can use instead of water when solvaiting 
> the system.

You can apply basically any conditions you wish.  genion will allow you to add 
any number of ions (and there are more than just Na+ and Cl-) that you wish. 
Simple stoichiometry and unit conversion can be done to calculate however many 
ions you may need to add.

pH is a different matter.  In classical simulations, a concept like pH does not 
directly apply, since protons cannot be exchanged.  You can set different 
protonation states for titratable residues when running pdb2gmx.  See the list 
in the manual and/or pdb2gmx -h.

If you want to solvate with something other than water, read this:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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