How to achieve NPT ensemble for sysytem containing rigid molecules

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1

Dear Lammps users/developers,

In my work, NPT ensemble is used to the simulation of a system consisting of organic acid, water, Na+ and Cl- and the organic molecules need to be kept rigid. I’m not sure whether I can use “rigid/npt” for organic molecule and “fix npt” for water and ions. Following is part of my “in” file.

fix a2 organic rigid/npt molecule temp $T $T 100 iso 1.0 1.0 1000

fix shk water shake 0.0001 50 100 b 5 a 5 t 8 9

fix b2 water npt temp $T $T 100.0 iso 1.0 1.0 1000.0

fix d2 nacl npt temp $T $T 100.0 iso 1.0 1.0 1000.0

Is it right? If not, how to modify?

I would appreciate any help and suggestion.

Thanks!

Zhang Chao

2

Dear Lammps users/developers,

In my work, NPT ensemble is used to the simulation of a system consisting of
organic acid, water, Na+ and Cl- and the organic molecules need to be kept
rigid. I'm not sure whether I can use “rigid/npt” for organic molecule and
“fix npt” for water and ions. Following is part of my “in” file.

fix a2 organic rigid/npt molecule temp $T $T 100 iso 1.0 1.0
1000

fix shk water shake 0.0001 50 100 b 5 a 5 t 8 9

fix b2 water npt temp $T $T 100.0 iso 1.0 1.0 1000.0

fix d2 nacl npt temp $T $T 100.0 iso 1.0 1.0 1000.0

Is it right? If not, how to modify?

why do you ask? have you even tried? yes? but you saw that the
simulation crashes, right?
have you searched the mailing list archives? this is a frequently
asked (and answered!) question!

I would appreciate any help and suggestion.

there is a whole section on the fix rigid documentation that discusses
these issues.

http://lammps.sandia.gov/doc/fix_rigid.html

the short version is, there may be *AT THE MOST* only one fix that
changes the box dimensions. you have three and that makes your
simulation bogus.

axel