On 4/26/15 7:07 PM, Agnivo Gosai wrote:
Hello Users, This is in relation to my previous posts. I am looking to replicate the figure below : tempgradient.png <https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web> Basically I am following this paper for my work : Lervik_ProtWatInterHT_2009.pdf <https://docs.google.com/file/d/0B-U8uULVZjfRU2haRkNHd2wwNTA/edit?usp=drive_web> Look at figure 6 of the paper. My system has water at 300 K and protein at 400 K. The authors of the paper describe that they removed the thermostat from the protein and let it relax keeping the solvent (water) at 300 K. But if I remove thermostat , I get GROMACS error and using freeze groups I am not getting any temperatures as the molecules are not moving.
You'll have to show us what you're doing to "get GROMACS error" (what error? what were your input settings? Don't make us guess!)
Freezing groups means they have no temperature and they don't move. This certainly isn't what you want.
I can not understand how to model this system. Any suggestions will be helpful. I am doing a literature search but till now it is not fruitful.
Setting tau_t = -1 for the protein tc-grp will "remove" the thermostat; e.g. not couple it. This sounds like what you want.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
