Previous Thread
Next Thread
Print Thread
can i run NPT simulation with charmm?
#23346 02/05/10 10:19 PM
Joined: Mar 2006
Posts: 18
P
Forum Member
OP Offline
Forum Member
P
Joined: Mar 2006
Posts: 18
I plan to put membrane, protein, water together and run simulations. I was suggested to run NAPzT simulaton (pressure is coupled only to z direction and the xy-corss area of the simulation box is a constant), because the force filed (c27) was optimized in NAPzT simulaton. I am wondering if i can run NPT simulation, where pressure is also coupled to xy direction with the newly developed charmm force field, such as c36? is c36 well developed so that i can use this force field just like c27?
thank you.

Last edited by parachuter; 02/05/10 10:20 PM.
Re: can i run NPT simulation with charmm?
parachuter #23347 02/05/10 10:29 PM
Joined: Dec 2005
Posts: 1,535
Forum Member
Offline
Forum Member
Joined: Dec 2005
Posts: 1,535
Ummm... there is a c36 force field for carbohydrates and the CHARMM general force field (CGenFF) was also released with c36, but you're only simulating "membrane, protein, water". Are you talking about the c32 lipid force field?

Re: can i run NPT simulation with charmm?
Kenno #23357 02/05/10 11:29 PM
Joined: Sep 2003
Posts: 8,582
Likes: 11
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,582
Likes: 11
The C36 lipid force field, which is suitable for NPT simulations, has not been released yet; the manuscript should be submitted for publication in the next couple of weeks.


Rick Venable
computational chemist

Re: can i run NPT simulation with charmm?
rmv #23358 02/05/10 11:40 PM
Joined: Mar 2006
Posts: 18
P
Forum Member
OP Offline
Forum Member
P
Joined: Mar 2006
Posts: 18
so, only c36 force field can be used to do NPT simulations? and it is well developed for NPT simulations with different kinds of lipids and amino acid (as long as these molecules are included in the force field)? thanks.
"The C36 lipid force field, which is suitable for NPT simulations, has not been released yet"

Re: can i run NPT simulation with charmm?
parachuter #23360 02/05/10 11:57 PM
Joined: Sep 2003
Posts: 8,582
Likes: 11
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,582
Likes: 11
NPT simulations of a range of PC lipid bilayers stay close to their expt area/lipid values for extended periods with the new c36 force field.

With the earlier c27 (and c32) lipid force fields, NPT simulations tend to condense in the xy plane, so that the area/lipid shrinks. To compensate, one can use the NPgammmaT ensemble with an applied surface tension (gamma) of about 15 dyn/cm.


Rick Venable
computational chemist

Re: can i run NPT simulation with charmm?
rmv #24454 05/30/10 05:45 PM
Joined: Jul 2004
Posts: 165
B
Forum Member
Offline
Forum Member
B
Joined: Jul 2004
Posts: 165
Dear Rick,

Is there any update for the C36 lipid force field?

Where can we get that?

Thank you very much

Re: can i run NPT simulation with charmm?
beginner #24455 05/30/10 06:16 PM
Joined: Sep 2003
Posts: 8,582
Likes: 11
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,582
Likes: 11
Since the paper is now available online (J. Phys. Chem. B, ASAP), the files are undergoing final review, and are about to be released on Alex MacKerell's site, maybe next week.


Rick Venable
computational chemist


Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.010s Queries: 28 (0.006s) Memory: 0.7472 MB (Peak: 0.8049 MB) Data Comp: Off Server Time: 2021-12-08 01:28:39 UTC
Valid HTML 5 and Valid CSS