Yeping Sun Institute of Microbiology, Chinese Academy of Sciences ------------------------------------------------------------------ 发件人：Justin Lemkul <jalem...@vt.edu> 发送时间：2013年10月27日(星期日) 20:27 收件人：gromacs <gmx-users@gromacs.org> 主 题：Re: 答复: [gmx-users] error in umbralla sampling step 6
Please keep the discussion on the list. On 10/27/13 5:09 AM, sunyeping wrote: > Dear professor Lemkul, > > For warning 1: > I use the npt_umbrella.mdp file you provided in step 6 in the umbralla > sampling > tutorial. You told us to start by running a brief NPT equilibration in each > window using this mdp file. If Parrinello-Rahman pressure coupling should be > used, why did you put it in the mdp file? > I know the tutorial system is robust enough that it won't matter. That is not necessarily true for whatever other system you come up with. Be careful when extrapolating something that works in a tutorial with something that is untested. The general logic is the same (you need to equilibrate for a little while first), but you have to think a bit about the proper settings. There is also no guarantee that the length of time I set in the tutorial simulation processes (equilibration, SMD, and umbrella sampling) will necessarily be sufficient for whatever you're doing. > For warning 2: > I check the gro files using vmd but I cann't find any molecule broken? How > can I > find the brroken molecule? The only way to find them is to look. I have no special advice for this. > I add -pbc whole option to the trjconv as following: > > trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep -pbc whole > > then It seems that the problemis solved. Is that a correct wayyou mean to > solve the problem? > Then clearly something was broken across PBC, which means there is no real problem. -JustinIn case that something was broken across PBC, why there is no real problem? Do you mean molecule breaking will not affect the simulation result? -- ================================================== Justin A. Lemkul, Ph.D. 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
