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
well.
Rabeta Yeasmin
On Mon, May 15, 2017 at 11:30 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> 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.
> -Josh
>
>
>
> On 05/14/2017 12:59 AM, Ajasja Ljubetič wrote:
> Hi,
>
> sure, I think distanceZ<https://na01.safelinks.protection.outlook.
> com/?url=https%3A%2F%2Fwww-s.ks.uiuc.edu%2FResearch%2Fnamd%
> 2F2.12%2Fug%2Fnode57.html%23SECTION000134120000000000000
> &data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C7d6bb15f161f44570f1b08d49a96
> b5e8%7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%
> 7C636303419467992956&sdata=PMue5PS%2FJ6PiSWGN%2BuEUvRQ%
> 2Fib5QgSSK4E99vYOJEIU%3D&reserved=0> colvar should fit your needs.
>
> Best,
> Ajasja
>
> On 14 May 2017 at 02:17, Rabeta Yeasmin <rabetayeasmin_at_gmail.com<mailto:
> rabetayeasmin_at_gmail.com>> wrote:
> Hi,
>
> 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?
> Thanks.
>
> Rabeta Yeasmin
>
>
>
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