[gmx-users] Umbrella sampling after TMD of NAMD

[Justin Lemkul]

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?
>>>
>>> Thank you in advance.
>>>
>>> Netaly Khazanov
>>> --
>>> Netaly
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> 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
>>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> 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
>>
>
>
>

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

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

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