Dear Vlad,
Thanks for your advise, it is greatly appreciated. I will definitely need to investigate this further.
Regards,
Fiona
________________________________
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of Vlad Cojocaru
Sent: Tuesday, 12 August 2008 6:45 PM
To: amber.scripps.edu
Subject: [!!!] - Re: AMBER: GPCR membrane simulation, setting surface tension - Message is from an unknown sender
Dear Fiona,
There is no option in Amber to add surface tension to your system (at least as far as I am aware of).As far as I know the article you cite here, only talks about POPC and not DPPC. Maybe you want to check the articles below as well. Even with the gaff force field, I would suggest you to use NAMD for your membrane simulations, as NAMD has more options regarding pressure control (including the surface tension option) and it accepts amber topologies as input. From the tests I have performed so far, doing NPT in AMBER with ntp=2 leads to more unrealistic membrane properties than doing NPT in NAMD with the Langevin piston method to control the pressure (if somebody has more experience here please carve in). Adding surface tension or not to the simulation is matter of debate. Its up to you to decide whether you really want to add it or not. It depends at which membrane properties you're looking at ... You should do some reading on the topic before deciding if you really want to add surface tension.
If you decide to use NAMD for the simulations please read very carefully the paragraph about using the AMBER force fields in NAMD (
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node15.html).
As a general remark, using gaff with membranes should still be regarded as experimental .. I am not saying here you shouldn't use it as I am using it myself but I would suggest lots of reading and first do a simulation only with the membrane to see how it behaves ...
Best wishes
vlad
Siu SW, Vácha R, Jungwirth P, Böckmann RA.
<
http://www.ncbi.nlm.nih.gov/pubmed/18376978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum>
Biomolecular simulations of membranes: physical properties from different force fields.
J Chem Phys. 2008 Mar 28;128(12):125103.
PMID: 18376978 [PubMed - indexed for MEDLINE]
Rosso L, Gould IR.
<
http://www.ncbi.nlm.nih.gov/pubmed/17910006?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum>
Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields.
J Comput Chem. 2008 Jan 15;29(1):24-37.
PMID: 17910006 [PubMed - indexed for MEDLINE]
Fiona McRobb wrote:
Dear Amber Users,
I am simulating a GPCR in a DPPC membrane, using AMBER 9 and I am using the recent journal article by Jójárt, 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 NPγT. 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.vcp.monash.edu.au <mailto:Fiona.McRobb.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
--
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Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Received on Sun Aug 17 2008 - 06:07:02 PDT
