[gmx-users] settingparameters for energy minimization

[vivek sharma]

Hi justin,
Thank you very much for your quick reply. I also want to know is there any
other option than PRODRG to generate topology files for the non-standard
residues ?
As PRODRG server usually go down these days.

With thanks,
Vivek

2009/3/2 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> vivek sharma wrote:
>
>> Hi There,
>> I am trying to do energy minimization of some protein molecule, and I have
>> following queries for the same.
>> 1. Can I define some RMSD tolerance, such that RMSD value of the molecule
>> during the energy minimization will not vary more than some predefined
>> value.
>>
>
> No, nor would it do much good.  Do you expect the RMSD to change much
> during EM?  I usually see an RMSD no greater than 0.2 Ang.
>
>  2. Which integrator is better to use SD or CG ?
>>
>
> That depends on your definition of "better."  Try both and see which
> results you think are more reliable, otherwise consult some textbook
> material or literature references on the algorithms.
>
>  3. what algorithm should be used for  long-range electrostatic interaction
>> PME or cut-off.
>>
>>
>
> PME is more accurate than cut-off.
>
> -Justin
>
>  Please suggest for the above queries.
>>
>> With thanks,
>> Vivek
>>
>>
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>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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