AW: keeping Crystal angles constant

From: Norman Geist (
Date: Thu Jan 16 2014 - 02:36:51 CST

If you want the crystal to periodic, the box size must fit with the crystal
constants. Otherwise the crystal is squeezed or will probably expand what
results in changed angles and average distances. Are there bonds and angle
parameters for this crystal?


Norman Geist.


Von: Mohan maruthi sena []
Gesendet: Donnerstag, 16. Januar 2014 09:34
An: Norman Geist
Betreff: Re: namd-l: keeping Crystal angles constant


Hello Sir,

              Thanks for a reply, The crystal is monoclinic and I am using
charmm parameters. The crystal is also periodic. I have given the correct
box size. Can you just elaborate how to mention the box size for crystal.




On Thu, Jan 16, 2014 at 1:43 PM, Norman Geist
<> wrote:

You should mention what kind of crystal and what set of parameters you use.
Do you have bond and angles defined or is it all nonbonded?


Usually, if the crystal is periodic in all directions and the box size is
correct, the angles shouldn't be able to deform. However, you might be
interested in the extrabonds command in namd.


Norman Geist.


Von: [] Im Auftrag
von Mohan maruthi sena
Gesendet: Mittwoch, 15. Januar 2014 19:04
Betreff: namd-l: keeping Crystal angles constant


Hi all,

          I want to simulate a crystal which has lengths a,b,c and angles
alpha=90 deg, beta=97.4 deg and gamma=90 degrees. When I minimize the
structure , i get a different structure whose alpha=90,beta =90 and
gamma=90. My question is , How can i keep alpha,beta,gamma constant in my
namd simulations. Do I have to mention any keyword in namd configurations

Thanks for a reply in advance,






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