[gmx-users] Re: distance restraints for atoms on 2 chains

[Sai Pooja]

Hi

This is regarding the pull code.. I have followed your tutorial to get the
PMF for distance between 2 atoms using the pull code. I want to know if one
can bring the atoms closer rather than pull them apart? I want to start from
the maximum distance and then bring them closer to check reversibility.
Also, I dont think I can apply it a fixed vector (as in specify the vector
from one atom to the other) because I dont think the path will be a straight
line.

Pooja

On Fri, Apr 1, 2011 at 8:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Sai Pooja wrote:
>
>> The pull tutorial uses npt simulations.. is that required by the algorithm
>> or can one use nvt after the system has been sufficiently equilibrated using
>> npt?
>>
>>
> Use whatever conditions are appropriate for your system.  Tutorials should
> not be viewed as the only applicable conditions, merely one such example of
> what might be done.
>
> -Justin
>
>  On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>    pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to
>>    create a merged [moleculetype] to apply distance restraints.  If
>>    you're just trying to use a harmonic potential to define some
>>    sampling distance (for US), then distance restraints are not
>>    necessary, just apply the pull code.
>>
>>    -Justin
>>
>>    Sai Pooja wrote:
>>
>>        Also, the chains do not diffuse apart in time since they are
>>        position restrained(some parts of each chain are ...)
>>
>>        On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja <saipooja at gmail.com
>>        <mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
>>
>>        <mailto:saipooja at gmail.com>>> wrote:
>>
>>           Hi,
>>                I have 5 chains in my Protein. I want to apply distance
>>        restraints
>>           for doing Umbrella Sampling for 2 atoms on different chains. Is
>>           there a way to do this since the two chains have separater
>>        itp files.
>>                Pooja
>>
>>           --     Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>
>>
>>        --         Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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-- 
Quaerendo Invenietis-Seek and you shall discover.
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