# [gmx-users] Umbrella sampling after TMD of NAMD

Justin Lemkul jalemkul at vt.edu
Wed Oct 17 14:37:21 CEST 2012

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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
>>
>> 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?
>>>
>>>
>>> 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

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

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