VMD-L Mailing List

From: Ekta Khurana (ekta_at_vitae.cmm.upenn.edu)
Date: Mon Feb 07 2005 - 13:57:23 CST

   Hi, I want to study the breaking of a dimer made up of two rings. Now
if I pull one COM away from the other(say ring 2) then either I can
keep one ring fixed or use no constraints on that(say ring 1).
1) If I keep ring 1 fixed then I bias the simulation as it is not fixed(
for some cases it is fine when one group of atoms is much heavier and thus
does not move, but in my case both rings have the same mass). If I could
keep atleast the COM of ring 1 fixed that could have been fine but using
Fixed Atoms parameter I fix all angles and dihedrals which are very
important for the process.
2) If I do not put any constraints on ring 1, then it moves randomly and
alongwith it ring 2.
  If I am wrong please correct me.
Thanks,
Ekta

> Hi,
> is it not the same thing ?
> when you pull away one center of mass from the other one, giving to it
> a velocity v, it's like
> you simultaneously pull away both with velocities v/2 and -v/2
> respectively
> Giovanni
>
>> Hello all,
>> I want to do SMD by pulling the center of mass of two groups of
>> atoms away from each other (two peptide rings). The way SMD is
>> currently implemented in NAMD I can only pull one away from the
>> other. Could someone suggest a solution for this? Can I use a TCL
>> script for the purpose?
>> Thanks in advance,
>> Ekta
>>
>>
> 

-- 
Ekta Khurana
Center for Molecular Modeling
University of Pennsylvania
email:ekta_at_cmm.upenn.edu
      ekhurana_at_sas.upenn.edu
Phone: (215) 573-8697
Fax: (215) 573-6233