[gmx-users] settingparameters for energy minimization
viveksharma.iitb at gmail.com
Mon Mar 2 14:25:43 CET 2009
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
As PRODRG server usually go down these days.
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
> 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.
> Please suggest for the above queries.
>> With thanks,
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> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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