Basically what I'm doing is pulling a ligand out of a protein towards a
dummy atom, which has a mass of 1 and no charge. I've attached the a
portion .mdp files for both the smd portion and the umbrella sampling. I
know that the ligand gets very close possibly crashing into the dummy
atom. So from what you're saying, I'm thinking this might be the source
of the problem.
- Laura
###### smd.mdp##########
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 123456
;COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry = distance
; Select components for the pull vector. default: Y Y Y
pull_dim = Y Y Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_start = yes
pull_nstxout = 10
pull_nstfout = 1
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0 =JJJ
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = CPZ
pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 =
pull_init1 =
pull_rate1 = -0.0006
pull_k1 = 800
pull_kB1 =
####### um.mdp ##############
;COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry = distance
; Select components for the pull vector. default: Y Y Y
pull_dim = Y Y Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_start = yes
pull_nstxout = 100
pull_nstfout = 100
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0 =JJJ
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = CPZ
pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 =
pull_init1 = 0
pull_rate1 = 0
pull_k1 = 1000
pull_kB1 =
On 07/02/2012 04:38 PM, Justin A. Lemkul wrote:
On 7/2/12 4:30 PM, Laura Kingsley wrote:
Just for clarification, the PMF is read from right to left and the force profile
is read from left to right.
The dramatic change in the magnitude and sign of the force, coupled with the
steady increase in PMF, indicates to me that some elements of your system are
crashing into one another. In the absence of an accompanying explanation of
what you're doing (description of system, procedure with .mdp parameters, etc)
that's the best I can offer.
-Justin
On 07/02/2012 04:27 PM, Kingsley, Laura J wrote:
Here is a link to both the PMF profile and the force profile:
http://s1064.photobucket.com/albums/u370/laurakingsley/?action=view¤t=pull_fig.jpg
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Justin A. Lemkul
Sent: Monday, July 02, 2012 3:56 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PMF trails off to infinity.
On 7/2/12 3:53 PM, Laura Kingsley wrote:
Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the
ligand until its COM is very close (a few angstroms) from the dummy atom. Could
this be causing this behavior? What information would help? I'm having a tough
Collisions between any elements of your system would explain the problem, if it
looks like what I'm picturing in my head :)
time getting the figures attached but may be I could email them directly to you?
Let me know.
Bullet point #4 here provides a suggestion:
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
-Justin
--
Laura Kingsley
Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643
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