Re: [gmx-users] msd and diffusion coefficient and getting unfolded trajectory
Hi, I did the calculation for water on both sides of bilayer. It is unlikely that water molecules donot cross the boundary. May be I need to wait for longer run such that molecules go out of box. I will check that. Thank you very much for your suggestions. Regards, Ananya. Ananya Debnath wrote: Hi, I want to calculate MSD (mean square displacement) for DPPC-WATER bilayer system, without using g_msd tool in gromacs, but using any other code, I need a trajcetory which is unfolded. From mails in mailing list I understand that people use trjconv -pbc nojump, to remove pbc. So I used pbc = xyz in .mdp file, and then trjconv -f traj.trr -s topol.tpr -o trajout.trr -pbc nojump Then if I calculate MSD (by my own code) from the trajout.trr , the result is same if I calculate from the original traj.trr file. Seeing the result I am confused, because -pbc nojump sholud stop the molecule from jumping across the box, then how can the MSD be same if it is with pbc? Maybe your trajectory does not have your relevant RMSD groups crossing the PBC, so trjconv is not doing anything relevant? Mark ___ gmx-users mailing listgmx-users@gromacs.org 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
RE: [gmx-users] Non integer charge for ARG and CYX?
Hi Eric Thanks for your reply. You are right, the charges in my ffamber03.rtp add up to +1 too. I got the ffamber 2003 ports for gmx331 from the site you mentioned. Actually, it was my mistake. When I transcribed the charges from the ffamber03.rtp to another file I missed the minus sign from the N atom...I'm sorry about that. Thanks again George Από: [EMAIL PROTECTED] εκ μέρους Eric J. Sorin Αποστολή: Σαβ 5/10/2008 12:48 πμ Προς: gmx-users@gromacs.org Θέμα: Re: [gmx-users] Non integer charge for ARG and CYX? Hi George, I just quickly checked the partial charges in ARG from the GROMACS v3.3.1 ffamber03.rtp file and the charges due indeed sum to +1, so I'm not sure why you're seeing non-integer total charge in the .rtp file it sounds like you might have a file that was modified by someone and maybe you need to update your ffamber files (?). Please tell me: Did you get these files from http://chemistry.csulb.edu/ffamber/? Which version of GROMACS are you using? Which set of ffamber ports (shown in the top of the .rtp file)? Thanks! Eric - Original Message - From: Georgios Patargias To: gmx-users@gromacs.org Sent: Thursday, May 08, 2008 4:09 AM Subject: [gmx-users] Non integer charge for ARG and CYX? Hello Sorry if I address an already covered issue. I happened to notice that adding up the ffamber03 partial charges for ARG doesnt yield +1 but ~1.6. Also, for CYX the total charge is ~0.87. Is this is a known issue? In the .itp file, pdb2gmx adds up rounded charge values (as seen in the qtot column) and so the total ARG charge comes up to +1 and for CYX 0. In .tpr, i.e. in the simulation, the full charge values are used, as they are contained in the ffamber03.rtp but grompp doesn issu warnings for non-integer total charge save for rounding errors. Thanks in advance. George Dr. George Patargias Polymer IRC Group University of Leeds Leeds, LS2 9JT, UK ___ gmx-users mailing listgmx-users@gromacs.org 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 ___ gmx-users mailing listgmx-users@gromacs.org 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 winmail.dat___ gmx-users mailing listgmx-users@gromacs.org 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
[gmx-users] RDF values lower than 1
Hi, i calculate the RDF from NVT simulation of a solution of polyelectrolyte chains and their counterions. The RDF calculated is between the monomers of the chains and the counterions. I would expect that the equilibrated value of RDF would be 1. However it is always lower than 1, at values of 0.9-0.95. Whats the reason of that , is anything wrong with my simulation? I do a long enough run to stabilize the total energy of the system and temperature Thanks in advance for your help Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org 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
[gmx-users] Melting temperature of the potato, a bug in grompp?
Dear grompp users, I can not reproduce the experimental melting temperature of the potato from the south east of my region! Even at 1 atm, for which the result is known. What is wrong with my trajectory? please help, XAvier - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org 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
