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:
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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