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

[Justin Lemkul]

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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

-- 
==================================================

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

==================================================