Please keep the discussion on the mailing list.
On 8/19/14, 5:14 AM, Mahboobe Sadr wrote:
Dear Dr.lemkul I used gromacs 453, but i didn't see any difference in these tutorial. And also I didn't see a problem like this anywhere to find out more about my problem. May I send you the files and bash history ?
No, all you need to do is copy and paste the commands you're giving. -Justin
Sent from myMail app for Android Monday, 18 August 2014, 09:15PM +0430 from Justin Lemkul <[email protected]>: On 8/18/14, 10:06 AM, Mahboobe Sadr wrote: > > Dear all, > I am new in gromacs and specially in MD simulation of membrane protein, in part "define box and solvent" of justin's tutorial , in scaling down the lipids, I reached an area per lipid of ~69 A^2, after 4 times instead of 26 times.... > I don't know ,where I made a mistake? Without seeing your exact commands and the corresponding output, there's nothing to say. If you scale each time by 0.95, it is mathematically impossible to arrive at a proper APL in this system with only 4 iterations. At least one of your commands or preparation steps was wrong; the outcome is extremely reproducible. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ==================================================
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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 [email protected].
