On 3/3/20 2:47 AM, Atila Petrosian wrote:
Dear Justin and Dallas, Thanks for your answers. I am so confused. I am beginner in MD simulation of lipid + small molecule. '' There are far better options for lipids than the old Berger parameters used in the tutorial. I wrote the tutorial in 2008 and it reflected a common protocol at the time ''. Justin, please suggest me better parameter for lipids, exactly (point out the web site).
I suggest you spend some time investigating the literature as many comparison studies have been done. This is a critical choice that you must make in designing your simulation study. The force field you choose needs to adequately cover all the elements of your system, not just the lipids.
'' Since you are using ATB to generate the topology for your small molecule, then it stands to reason that you then should use ATB for the lipid molecule. '' Dallas, are you sure ATB can be used for lipids ???
Here I disagree with Dallas. Any robust force field already supports lipids and you should not have to rely on ATB to produce the lipid parameters, which will likely be less accurate than specifically parametrized entities.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
