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

[Sai Pooja]

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?

On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul <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>> 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 | (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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