[gmx-users] How to write pull code in umbrella sampling

[Qing Lv]

Thank you so much, Justin. I will look into PLUMED.


Qing


At 2017-04-08 19:05:28, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 4/8/17 1:46 AM, Qing Lv wrote:
>> Thank you, Justin.
>>
>>
>> My goal is to investigate the conformation transition of a 30aa loop between an unstructured loop and an alpha-helix. I found a transition pathway on free energy landscape and selected a number of frames along the pathway for umbrella sampling. So, should I define C-alpha of this 30aa loop as pull-group1 and C-alpha of the remaining part as pull-group2 ? Would the pull geometry still be "distance"? But this will just restrain the distance between COM of the 2 groups to the initial distance, but cannot restrain the conformation of the loop.
>> Or need I divide the loop into many small segments (pull-groups) and define the pull coordinates separately? This seems horrible...
>>
>
>You should probably be looking at a more advanced, multi-dimensional bias or 
>collective variable.  Look into PLUMED.  GROMACS is going to be limited to a 
>linear reaction coordinate, which may not capture everything you need in such a 
>large transition.
>
>-Justin
>
>>
>> Thanks,
>> Qing
>>
>>
>> At 2017-04-08 09:06:46, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>>
>>>
>>> On 4/7/17 8:56 PM, Qing Lv wrote:
>>>> Dear Colleagues,
>>>>
>>>>
>>>> I am trying to do an umbrella sampling using a series of conformations extracted from several unbiased MD trajectories. But I am not sure about the pull code in .mdp file.
>>>> Below is the pull code from the tutorial of Dr. Justin Lemkul :
>>>> define      = -DPOSRES_B ; (Why ??)
>>>
>>> Did you read the paper I linked from the tutorial, which explains why this is
>>> done for this very specific case?
>>>
>>>> ; Pull code
>>>> pull                    = yes
>>>> pull_ngroups            = 2
>>>> pull_ncoords            = 1
>>>> pull_group1_name        = Chain_B
>>>> pull_group2_name        = Chain_A
>>>> pull_coord1_type        = umbrella      ; harmonic biasing force
>>>> pull_coord1_geometry    = distance      ; simple distance increase
>>>> pull_coord1_groups      = 1 2
>>>> pull_coord1_dim         = N N Y
>>>> pull_coord1_rate        = 0.0
>>>> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
>>>> pull_coord1_start       = yes           ; define initial COM distance > 0
>>>>
>>>>
>>>>
>>>> Conformations in Justin's tutorial are from steered MD. However, my conformations are not from SMD, and I have not done SMD on this system. So, how to define pull_group1 and pull_group2? And pull_coord1_geometry still set to "distance" ?
>>>
>>> The pull groups don't depend on where the configurations came from.  They define
>>> the reaction coordinate.  You can use whatever pull geometry makes sense; in the
>>> tutorial it is a simple linear reaction coordinate directly along the z-axis.
>>> Other applications may require different definitions.
>>>
>>>> Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? Why?
>>>
>>> Generally, no, but you haven't given any useful detail about what your
>>> simulation system is.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
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>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==================================================
>-- 
>Gromacs Users mailing list
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