[gmx-users] Umbrella sampling after TMD of NAMD

[Netaly Khazanov]

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



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
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>
>>>>  --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> * Please search the archive at
>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>
>>>
>>
>>
>>
> --
> ==============================**==========
>
> 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>
>
> ==============================**==========
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
Netaly