[gmx-users] Umbrella sampling after TMD of NAMD

[Justin Lemkul]

On 10/17/12 9:17 AM, Netaly Khazanov wrote:
> Thanks.
>
> However, I can restrain the position of backbone (x,y,z -coordinates) while
> running umbrella sampling and treat it like reaction coordinate. Is it
> right?
>
> Maybe  I am missing something.
>
> pull = umbrella
> pull_geometry = position
> ;pull_dim = Y Y Y
> pull_start = yes
> pull_ngroups = 1
> ;pull_group0 =0
> pull_group1 = backbone
> pull_init1 = 0
> pull_rate1 = 0.0
>

With this approach, you restrain the backbone with respect to no specific group 
(i.e. an absolute restraint), so the PMF is based on the position of the 
backbone of the protein, not the value of its RMSD.

-Justin

>
>
> On Wed, Oct 17, 2012 at 2:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/17/12 5:44 AM, Netaly Khazanov wrote:
>>
>>> Of course I read Justin's tutorial.
>>> The reason I am asking is that I am not sure how to do it.
>>>
>>>
>> As far as I am aware, there is no way to conduct umbrella sampling in this
>> way using Gromacs.  The PMF calculations that Gromacs does are based on
>> restrained distances or angles.  I do not believe one can set an arbitrary
>> variable like RMSD to be a reaction coordinate in the same sense, and
>> certainly the pull code is not applicable in this instance.
>>
>> -Justin
>>
>>
>>   On Wed, Oct 17, 2012 at 11:09 AM, Arman Mahboubi Soufiani <
>>> armansoufiani at gmail.com> wrote:
>>>
>>>   Hi,
>>>>
>>>> I recommend you Justin's tutorial on Umbrella Sampling
>>>>
>>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
>>>> gmx-tutorials/umbrella/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html>
>>>>
>>>> Regards
>>>>
>>>> Arman
>>>>
>>>> On Wed, Oct 17, 2012 at 10:47 AM, Netaly Khazanov <netalyk at gmail.com>
>>>> wrote:
>>>>
>>>>   Dear All,
>>>>>
>>>>> I've performed TMD simulation using NAMDprogram. I'd like to calculate
>>>>>
>>>> PMF
>>>>
>>>>> plot based on the frames that were taken from TMD simulations by using
>>>>> GROMACS.
>>>>> The  coordinate  of reaction is RMSD of backbone.
>>>>> The first step is to do Umbrella sampling. The question is how fix the
>>>>> position of backbone during the Umbrella sampling?
>>>>> Is this looks reasonable?
>>>>>
>>>>> pull            = umbrella
>>>>> pull_geometry   = position
>>>>> ;pull_dim        = Y Y Y
>>>>> pull_start      = yes
>>>>> pull_ngroups    = 1
>>>>> ;pull_group0     =0
>>>>> pull_group1     = backbone
>>>>> pull_init1      = 0
>>>>> pull_rate1      = 0.0
>>>>> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>>>>> pull_nstxout    = 1000      ; every 2 ps
>>>>> pull_nstfout    = 1000      ; every 2 ps
>>>>>
>>>>> Any ideas how to convert the reaction coordinate from position of
>>>>>
>>>> backbone
>>>>
>>>>> to RMSD of backbone in PMF plot?
>>>>>
>>>>> Thank you in advance.
>>>>>
>>>>> Netaly Khazanov
>>>>> --
>>>>> Netaly
>>>>> --
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>>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>>
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>
>
>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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