[gmx-users] NMA for a group
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 22 10:53:03 CEST 2007
Christian Seifert wrote:
> Perhaps, I made a mistake in describing my problem. I can not believe, that no
> one ever tried this before.
> I have a phosphate in water and want to calculate the hessian just for the
> phosphate. How do I do that?
there is a contradiction here in that you say the phosphate is in water
and you want to do the NMA for just the phosphate. Something like that
might work with a continuum solvent but I don't know how you would do it
with explicit solvent.
> On Tuesday 19 June 2007 14:39, Christian Seifert wrote:
>> I want to make a NMA just for one Group of molecules, because a QMMM-NMA
>> takes too long for the whole system. Of cause, the EM in the step before
>> has been done for the whole system. The manual does not tell how to do
>> this. Did someone tried this before?
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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