Hi Alif, Probably papers from Alex de Vries and Siewert-Jan Marrink will be good to start with (mind not to take the coarse-grained ones, unless that's what you want to do ;)) Also consider that self-assembly is not really different from bilayer/monolayer simulations.
Best, Tsjerk On 8/29/07, Syma Khalid <[EMAIL PROTECTED]> wrote: > > > > > Hi, > > > > The GROMACS user manual is a good place to start. For more specific help you > will probably need to provide details of exactly what you want to do. > > What are you simulating? What are the questions you are hoping to answer? > > > > > > Best wishes, > > > > -Syma > > > > > ******************************************************************** > > Dr. Syma Khalid e-mail: [EMAIL PROTECTED] > Dept. of Biochemistry phone: (0)1865-275380 > University of Oxford fax: (0)1865-275273 > South Parks Road > Oxford > OX1 3QU > U.K. > ________________________________ > > ________________________________ > > > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Alif M Latif > Sent: 29 August 2007 19:19 > To: [email protected] > Subject: [gmx-users] Self-assembly lipid simulation > > > > > > Dear Gromacs users, > > > > > > I'm doing MD Simulation on self-assembly of lipid molecules using gromacs. > If someone can kindly help me find the conditions (for my .mdp file) for > these kind of simulation? There are many choices and i would like to ask for > opinion on general (usually) conditions used in the .mdp file for the > simulation. I would like to look for physical and some thermodynamical > properties from my simulation results. This is to aid the experimental > results done. > > > > > > Any paper or links also can help me a lot. I have read many papers but i > thought maybe u guys can help add more to it. This is because not much > options i can find in those papers and not all of them use gromacs.Thanks > for reading and your help is greatly appreciated. Thanks again. > > > > > > ---------------------------------------------------------------------------------------------------------------------------------- > > > > > > M. Alif M. Latif > > > Chemistry Department, Faculty of Science, > > > Universiti Putra Malaysia, > > > 43400 UPM Serdang, Selangor, > > > Malaysia > > > ________________________________ > > > Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, > news, photos & more. > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
