From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon May 15 2017 - 11:30:55 CDT
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 Ljubeti 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%7C7d6bb15f161f44570f1b08d49a96b5e8%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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