AMBER Archive (2008)

Subject: AMBER: GPCR membrane simulation, setting surface tension

From: Fiona McRobb (Fiona.McRobb_at_vcp.monash.edu.au)
Date: Mon Aug 11 2008 - 20:42:47 CDT

Dear Amber Users,
 
I am simulating a GPCR in a DPPC membrane, using AMBER 9 and I am using the recent journal article by J¨®j¨¢rt, B., et al. (J. Chem. Inf. Model. 2008, 48(6), 1199-1210.) as a guide for the simulation conditions.
 
Following minimisation, I have heated the system to 310K using NVT ensemble. I will then be running equilibration dynamics and I am trying to determine the best type of ensemble to use, either NPT or NP¦ÃT. Hence, I will be running simulations with both types of ensembles to determine which one I should use. Which brings me to my question - is it possible to set the surface tension in AMBER and if it is possible, which settings do I need to employ to achieve this? Being a new user of AMBER, I have looked through the manual extensively for the method to set the surface tension, but I have been unable to find the setting I am looking for.
 
Any help or suggestions would be greatly appreciated,
 
Regards,
 
Fiona
 
 
Fiona M. McRobb B.Med.Chem.(Hons)
PhD Candidate
Phone: +61 3 99039165
Email: Fiona.McRobb_at_vcp.monash.edu.au <mailto:Fiona.McRobb_at_vcp.monash.edu.au>
 
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia

 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu