[gmx-users] Umbrella sampling after TMD of NAMD
jalemkul at vt.edu
Wed Oct 17 14:37:21 CEST 2012
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.
> On Wed, Oct 17, 2012 at 11:09 AM, Arman Mahboubi Soufiani <
> armansoufiani at gmail.com> wrote:
>> I recommend you Justin's tutorial on Umbrella Sampling
>> On Wed, Oct 17, 2012 at 10:47 AM, Netaly Khazanov <netalyk at gmail.com>
>>> Dear All,
>>> I've performed TMD simulation using NAMDprogram. I'd like to calculate
>>> plot based on the frames that were taken from TMD simulations by using
>>> 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
>>> to RMSD of backbone in PMF plot?
>>> Thank you in advance.
>>> Netaly Khazanov
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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