Alok, If you want to see the symmetry as in the crystal, try and simulate the crystal. It may well be that in the absence of crystal packing forces a certain degree of asymmetry is favourable.
Tsjerk On Sat, Jul 5, 2008 at 12:54 AM, Alok Sharma <[EMAIL PROTECTED]> wrote: > Dear All, > > I have two queris > First: > > I am simulating a tetramic protein, each monomer with 150 amino acids, in > gromacs 3.3.1. The protein molecule has a proper 4 fold symmetry. But during > simulation the symmetry is some what not retained. Two monomers which should > be > related by ~180 degree rotation, as seen in all the crytal structuers of the > protein, gets oriented ~160 degrees. I am just wondering whether in gromcas > there is an option to restrict/restrain the symmetry of the molecule (similar > to > non-crystallographic symmetry in crystallographic refinments). One way of > doing > this seems to restrain the back-bone which is not desired in the present case. > Can any body suggest a way to restrain monomers, just to maintain the > symmetry? > > Second: > For a 20 ns simulation trajectory I want to calculate water mediated hydrogen > bonds between two monomers. I used -ins flag with g_hbond with following > command... > > g_hbond -f protein.xtc -s protein.tpr -n index.ndx -ac -dist -ang -hx -hbn > -hbm > -don -dan -life -nhbdist -ins -a 30 -r 0.36 -da. > All the calculations are okay. Also an insert.dat file is created but it does > not show any solvent insertion. I selected solvent group also for insertion > correctly when prompted. But at least with some of the snap shots which I > saw, I > can find water mediated hydrogen bonds...Is there any other way to calculate > solvent mediated hydrogen bonds.. > > > Thanks in advance for your suggestions > > Alok > > > > > > > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
