[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:
> Hi.
> 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.
> Regards,
> Christian
> On Tuesday 19 June 2007 14:39, Christian Seifert wrote:
>> Hi.
>> 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?
>> Thanks
>> Christian.

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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