[gmx-users] non squares box
Dear All, I would like to ask your help on the following - I want my simulation to include a surface, and have PBC. The surface I chose is aligned on the XY plane. However, the surface is not a square. The surface dimensions are a=b=169.2 c=6.9 Angstroms, the angles are: bc=ac=90 ab=120 degrees. I have used editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0. To test this, I have used trjconv -pbc nojump -center yes -boxcenter zero. My problem is that the trjconv generates a structure where some of the surface atoms are cut and/or overlapping... Could you please help me? Wheres the problem? The input PDB I use is about 2 MB in size, so it can't be attached here. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-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
Re: [gmx-users] non squares box
Hi Omer, To check your periodicity use genconf: genconf -f in.pdb -o out.pdb -nbox 2 2 2 Cheers, Tsjerk On Sun, Jun 21, 2009 at 11:23 AM, Omer Markovitchomer...@gmail.com wrote: Dear All, I would like to ask your help on the following - I want my simulation to include a surface, and have PBC. The surface I chose is aligned on the XY plane. However, the surface is not a square. The surface dimensions are a=b=169.2 c=6.9 Angstroms, the angles are: bc=ac=90 ab=120 degrees. I have used editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0. To test this, I have used trjconv -pbc nojump -center yes -boxcenter zero. My problem is that the trjconv generates a structure where some of the surface atoms are cut and/or overlapping... Could you please help me? Wheres the problem? The input PDB I use is about 2 MB in size, so it can't be attached here. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing list gmx-us...@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 -- 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 listgmx-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
Re: [gmx-users] non squares box
Omer Markovitch wrote: Thanks. I am not sure how this addresses my problem. I am getting broken structure at the end of the MD (in confout.gro), Well, you didn't say you were doing MD. I (and presumably Tsjerk) thought you were converting your output from editconf. In such a case, Tserk's suggestion lets you tile some boxes together to see how things are (not) working. Your results will also depend on the contents of your editconf -f file.gro. I suggest you copy and paste your actual commands in future :-) Mark and want to be sure that GMX treat it correctly during the MD. To check your periodicity use genconf: genconf -f in.pdb -o out.pdb -nbox 2 2 2 ___ gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] non squares box
Right, there was no reference whatsoever to MD. The first sentence, preluding the problem, mentioned editconf. The second, mentioned trjconv. No grompp/mdrun etc in between. Anyway, also to check the periodicity in your output (note how flexibly I adapt it to the current situation): genconf -f confout.gro -o out.pdb -nbox 2 2 2 :p Tsjerk On Sun, Jun 21, 2009 at 1:33 PM, Mark Abrahammark.abra...@anu.edu.au wrote: Omer Markovitch wrote: Thanks. I am not sure how this addresses my problem. I am getting broken structure at the end of the MD (in confout.gro), Well, you didn't say you were doing MD. I (and presumably Tsjerk) thought you were converting your output from editconf. In such a case, Tserk's suggestion lets you tile some boxes together to see how things are (not) working. Your results will also depend on the contents of your editconf -f file.gro. I suggest you copy and paste your actual commands in future :-) Mark and want to be sure that GMX treat it correctly during the MD. To check your periodicity use genconf: genconf -f in.pdb -o out.pdb -nbox 2 2 2 ___ gmx-users mailing list gmx-us...@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-us...@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 -- 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 listgmx-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
Re: [gmx-users] non squares box
I prefer to keep discussions professional, Mark and Tsjerk. Anyway, I am doing MD with PBC. I have a surface which sits on the XY axes, the surface is not a square and my question is how do I tell gromacs that I have a non standard box. Please see my original post for more details: ++ I would like to ask your help on the following - I want my simulation to include a surface, and have PBC. The surface I chose is aligned on the XY plane. However, the surface is not a square. The surface dimensions are a=b=169.2 c=6.9 Angstroms, the angles are: bc=ac=90 ab=120 degrees. I have used editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0. To test this, I have used trjconv -pbc nojump -center yes -boxcenter zero. My problem is that the trjconv generates a structure where some of the surface atoms are cut and/or overlapping... ++ Thank you. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-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
Re: [gmx-users] non squares box
Omer Markovitch wrote: I prefer to keep discussions professional, Mark and Tsjerk. Anyway, I am doing MD with PBC. I have a surface which sits on the XY axes, the surface is not a square and my question is how do I tell gromacs that I have a non standard box. Please see my original post for more details: Dear Omer, I agree with Tsjerk that genconf is a useful tool to visualize the periodicity using PyMol, as was suggested. If you dismiss this kind of advice and repeat the original question, people get upset. What you are saying is that you generated a box using editconf, but editconf does not put the atoms in the box. Hence putting a box that does not correspond to the coordinates will give rise to atomic clashes. I'm not quite sure what you think should be the expected result of your trjconv operation. ++ I would like to ask your help on the following - I want my simulation to include a surface, and have PBC. The surface I chose is aligned on the XY plane. However, the surface is not a square. The surface dimensions are a=b=169.2 c=6.9 Angstroms, the angles are: bc=ac=90 ab=120 degrees. I have used editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0. To test this, I have used trjconv -pbc nojump -center yes -boxcenter zero. My problem is that the trjconv generates a structure where some of the surface atoms are cut and/or overlapping... ++ Thank you. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-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.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
