[gmx-users] PMF trails off to infinity.

[Laura Kingsley]

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&current=pull_fig.jpg
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at 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