On 10/28/12 8:50 AM, vidhya sankar wrote:
Dear justin,
Thank you For your Previous reply
I am doing Lipid -protein Bilayer simulation. As instructed in your tutorial
i Have done Shrinking And EM .until i have Attained Area per Lipid 62.36A.
Then I Have solvated as in the Tutorial ( using Vadradii 0.375) using Genbox
tool
As result My system has Solvated with 74496 Solvent Molecules . This is Too
Higher for My system
Is there is any Gromacs tools or other server or Package Available to delete
Excess Water molecules . I wanted to Keep Water Molecules only on Either side
of Bilayer While I need to Delete Water Molecules Nearer to Protein and
deep inside the box ( box size 6 6 6)
There is no way that 70000 water molecules can fit in a 6-nm cubic box; it's
about an order of magnitude higher than what you achieve with a pure water
system. None of this makes any sense to me. If you need to remove water
molecules, there are scripts for that:
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
When i Try to solvate With Lower Number of Molecules ( 2000 Molcules) Which
need to be Kept On either side of Bilayer ,
Then I need to Continue Shrinking process There by It is getting Over
compressed ( Area Per Lipid Become Less than Experimental Value)
Certainly if you continue shrinking, you will overcompress the APL. I would
suspect that at some point the energy minimization does not produce very good
results though (high forces and bad energies).
Also When I solvate with Experimental APL 62A Then My system become over
solvated ? How to rectify this Problem
I have never had a problem with a membrane being over-solvated if the APL is
correct. Maybe a few stray water molecules, but nothing to the extent you're
claiming.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
