On 7/12/13 2:28 PM, Shima Arasteh wrote:
Thanks for your replies. :-)
So, if I want to the ion move in only z-direction, I need to set the 'pull_dim'
Y Y N? Correct?
But in tutorial Justin writes : pull_dim = N N Y: we are pulling only in the z-dimension. Thus, x
and y are set to "no" (N) and z is set to "yes" (Y).
So what should I do?!
The pull_dim setting is irrelevant when using position geometry. Only pull_vec1
matters here.
-Justin
Sincerely,
Shima
----- Original Message -----
From: Thomas Schlesier <schl...@uni-mainz.de>
To: gmx-users@gromacs.org
Cc:
Sent: Friday, July 12, 2013 9:04 PM
Subject: [gmx-users] Re: Umbrella Sampling settings
In GROMACS groups are called via the *.ndx file (default: index.ndx)
Be aware that 'pull_dim' determines in which diretions (x,y,z) the
umbrella potential acts. So use N N Y , if you want that the ion can
move freely (onsidering the pull) in the xy-plane and Y Y Y if you want
to also restrit the movement in the xy-plane.
Am 12.07.2013 17:32, schrieb gmx-users-requ...@gromacs.org:
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?
Thanks for all your time and consideration.
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul<jalem...@vt.edu>
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Cc:
Sent: Friday, July 12, 2013 1:41 AM
Subject: Re: [gmx-users] Umbrella Sampling settings
On 7/11/13 5:10 PM, Shima Arasteh wrote:
Thanks for your reply.
But when I don't understand why these extra lines are needed to set when are
not advantageous practically!:-(
There's nothing "extra."? Everything here has a functional purpose.
-Justin
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul<jalem...@vt.edu>
To: Shima Arasteh<shima_arasteh2...@yahoo.com>; Discussion list for GROMACS
users<gmx-users@gromacs.org>
Cc:
Sent: Friday, July 12, 2013 1:37 AM
Subject: Re: [gmx-users] Umbrella Sampling settings
On 7/11/13 4:21 PM, Shima Arasteh wrote:
Hi,
I want to run Umbrella Sampling on my system. In initial configurations, an ion
is located in center of the window.
Some mdp file settings for running US, as I found in US tutorial are :
; Pull code
pull? ? ? ? ? ? = umbrella
pull_geometry?? = distance
pull_dim? ? ? ? = N N Y
pull_start? ? ? = yes
pull_ngroups? ? = 1
pull_group0? ?? = Chain_B
pull_group1? ?? = Chain_A
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
But I'd like to know which lines are specifically for US? Because in this step,
no group is supposed to be pulled but there are some lines written here related
to pulling!
All of them are related to umbrella sampling.? Pulling (steered MD) and umbrella
sampling simply use common parts of the "pull code" in Gromacs because US
requires a restraint potential.? Whether or not that restraint potential induces
net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate,
restrain to a given set of conditions) is the only difference.? Both processes
require reference and "pull" groups, geometry information, etc.
-Justin
--
==================================================
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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