On 7/12/13 11:32 AM, Shima Arasteh wrote:
Allright.
As I said earlier, my system is a lipid bilayer. A channel is inserted in it
and I want to run US on this system.
An ion is considered in center of the each window, the reaction coordinate is
set to z, so the group which is pulled is an ion, and my ref group would be
COM of the protein. But I don't know what statement is supposed to write in mdp
settings exactly:
; Pull code
pull = umbrella
pull_geometry = position
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = COM of protein
pull_group1 = ion
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 4000 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
IN fact, to implement such settings, how I make the US understand to get the
COM of protein as the ref group and the proposed ion as the pulled group?
Would you please give me any suggestions?
You got a very thorough response already today:
http://lists.gromacs.org/pipermail/gmx-users/2013-July/082855.html
I see that your settings are now different, using "position" geometry instead of
"distance," which is good because that's a better approach for your system.
What you haven't specified is pull_vec1, which is necessary when using
"position" geometry.
All of these details are discussed to some extent in my umbrella sampling
tutorial; it should certainly serve as a basic guide. What you're trying to do
is ultimately going to require a slightly different approach, but the general
principles and explanations of .mdp terms are the same.
-Justin
--
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Justin A. Lemkul, Ph.D.
Postdoctoral Associate
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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