From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Mon May 15 2017 - 13:19:33 CDT
Thanks so much. I have already used harmonic constrain stuff and it worked
On Mon, May 15, 2017 at 11:30 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> Alternatively, you can also tag specific atoms and then use the normal
> harmonic restraint stuff. So in VMD, it would be:
> set allsel [atomselect top "all"]
> $allsel set beta 0
> set restrainsel [atomselect top "name C21 C31"]
> $restrainsel set beta 1
> $allsel writepdb tag.pdb
> And then in NAMD do as follows:
> contraints on
> consref tag.pdb
> conskfile tag.pdb
> conskcol B
> selectConstraints on
> selectConstrZ on
> Combined, this will apply a hamonic potential with a 1kcal/mol/Angstrom^2
> force constant to the C21 and C31 atoms to restrain them to their initial
> positions in the pdb.
> On 05/14/2017 12:59 AM, Ajasja Ljubetič wrote:
> sure, I think distanceZ<https://na01.safelinks.protection.outlook.
> 2Fib5QgSSK4E99vYOJEIU%3D&reserved=0> colvar should fit your needs.
> On 14 May 2017 at 02:17, Rabeta Yeasmin <rabetayeasmin_at_gmail.com<mailto:
> rabetayeasmin_at_gmail.com>> wrote:
> I want to constrain z coordinates of some selected atoms. The NAMD user
> manual showed one option which is for restraing the z coordinates for all
> atoms. Can anyone please tell me if there is any way to restrain selected
> atoms z coordinates?
> Rabeta Yeasmin
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