But i am in a situation like the minimization doesn't make any change in the energy and it convergeing at 15 th step each time. So further minimization is not possible. Can you plz check the em.mdp file and tell me whetehr I have given any wrong parameter?
Dept. Biotechnology Ext. 3108 ----- Original Message ----- From: "XAvier Periole" <x.peri...@rug.nl> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent: Saturday, June 20, 2009 7:16:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] Coordinates change after minimization On Jun 20, 2009, at 15:30, "Ms. Aswathy S" <aswat...@amritapuri.amrita.edu > wrote: > using the g_confrm command the RMSD of the protein is 0 (Root mean > square deviation after lsq fit = 4.14581e-08). It means the > structure doesn't have a major change ultimately.. Please correct me > if I am wrong.. You are correct. > Can I move ahead with this minimization? However this value is really small, which suggests that the minimization did actually about nothing. This a bit too nothing! Of I were you I would check that you actually used g_confrm the right way or indeed performed a minization. > > Dept. Biotechnology > Ext. 3108 > > ----- Original Message ----- > From: "David van der Spoel" <sp...@xray.bmc.uu.se> > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Sent: Saturday, June 20, 2009 6:07:20 PM GMT +05:30 Chennai, > Kolkata, Mumbai, New Delhi > Subject: Re: [gmx-users] Coordinates change after minimization > > Justin A. Lemkul wrote: >> >> >> Ms. Aswathy S wrote: >>> Hi, >>> >>> After minimizing the protein -ligand complex, the co-ordinates have >>> changed >>> drastically.My idea about minimization was the coordinates will have >>> minute >>> changes only. In this case my protein is completely transferring >>> to a new >>> co-ordinates.Is that reasonable.?? >> >> The amount of change will depend on the quality of the initial model. >> If large changes need to be made, they can be. If the entire >> protein is >> moving, then perhaps the box has not been prepared correctly, and the >> translation is caused by a periodic jump. Have a look at the output >> (not just the coordinates) and see if you can deduce what's going on. >> > Try running g_confrms to see whether they really are very different. > >> -Justin >> >>> >>> Thanks, Aswathy Dept. Biotechnology Ext. 3108 >>> _______________________________________________ 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/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/mailing_lists/users.php >>> >> > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++ > _______________________________________________ > 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/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/mailing_lists/users.php > _______________________________________________ > 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/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/mailing_lists/users.php _______________________________________________ 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/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/mailing_lists/users.php
em_old.mdp
Description: Binary data
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