[gmx-users] maxwell-boltzmann distribution
Hi dear GROMACS experts I wanna know if GROMACS uses only Maxwell-Boltzmann distribution in statistical mechanics, or it also uses Fermi-Dirac and Bose-Einstein statistics.If it only uses Maxwell-Boltzmann distribution, are the results reliable and correct? I mean can we use this law, which is based on the Kinetic Theory of Gases, for a system containing protein (that is not in gaseous state)? If we can use it, why? Bests -Zahra -- gmx-users mailing listgmx-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] calculating lennard-jones interaction
hi dear users wanna know if the distance between two species is more than the cut off radius of vdw interaction (in a SMD simulation), can we trust the simulation results? I mean what is the difference between this case and the situation that the cut off radius is lower than the distance between two species. bests. Zahra -- gmx-users mailing listgmx-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] positive potential energy
Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing, after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error. thank you in advanced Bests -Zahra -- gmx-users mailing listgmx-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] Re: positive potential energy
Sorry ...I forget to announce that my potential energy is positive, is it logical? From: Zahra M s_zahra_mous...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, December 29, 2011 12:52 PM Subject: positive potential energy Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing, after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error. thank you in advanced Bests -Zahra-- gmx-users mailing listgmx-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] Re: gmx-users Digest, Vol 92, Issue 138
From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Thursday, December 29, 2011 1:05 PM Subject: gmx-users Digest, Vol 92, Issue 138 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: -pbc nojump (mohammad agha) 2. positive potential energy (Zahra M) 3. Re: positive potential energy (Zahra M) 4. Re: Re: positive potential energy (Mark Abraham) -- Message: 1 Date: Wed, 28 Dec 2011 18:54:54 -0800 (PST) From: mohammad agha mra...@yahoo.com Subject: Re: [gmx-users] -pbc nojump To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 1325127294.34356.yahoomail...@web125705.mail.ne1.yahoo.com Content-Type: text/plain; charset=us-ascii Thank you very much from your reply. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 29, 2011 1:56 AM Subject: Re: [gmx-users] -pbc nojump Hi Sara, Please keep discussions on the list. I'm not your private tutor. Whether you can do your analysis depends on the analysis you want to do. But if your aim is analyzing the formation of the micelle, you're probably better of reversing the trajectory. 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole -s md.tpr This makes molecules whole, which is fine. Clustering should make molecules whole too, though, making this step redundant. 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 60 -pbc cluster Fine, you get a cluster 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro This does nothing special. Just because you have a reference clustered doesn't mean the output frame will turn out clustered. 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc nojump This screws up everything. You can only use -pbc nojump with a reference structure that is sufficiently close to the first frame of the trajectory. Your reference is a snapshot at t=600 ns. 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o cluster3.xtc This would probably be fine if the trajectory was okay there. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20111228/d0b386d6/attachment-0001.html -- Message: 2 Date: Thu, 29 Dec 2011 01:22:15 -0800 (PST) From: Zahra M s_zahra_mous...@yahoo.com Subject: [gmx-users] positive potential energy To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 1325150535.62665.yahoomail...@web161705.mail.bf1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing, after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error. thank you in advanced Bests -Zahra -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20111229/d842ec1a/attachment-0001.html -- Message: 3 Date: Thu, 29 Dec 2011 01:24:14 -0800 (PST) From: Zahra M s_zahra_mous...@yahoo.com Subject: [gmx-users] Re: positive potential energy To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 1325150654.64323.yahoomail...@web161705.mail.bf1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Sorry ...I forget to announce that my potential energy is positive, is it logical? From: Zahra M s_zahra_mous...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, December
[gmx-users] dodecahedron box
hi dear all users I'm simulating 2 proteins in a dodecahedron unit cell,and I want to put these 2 proteins in an exact distance from each other, and also from the boundaries, and I have some questions for doing this. 1) How can I implement this exact distance from the other protein and also the edges of the box? 2) when I use dodecahedron unit cell with this command: editconf -f protein.gro -o protein_newbox.gro -bt dodecahedron -d 1.0 -c, the first protein is in the center of the box, but as I want to add the second protein at the distance of 1.0 nm from the first one, I decided to determine box vectors and protein position myself, and I wrote: editconf -f protein.gro -o protein_newbox.gro -box 4 4 6 -angles 60 60 90 -center 2 2 2, but a part of protein becomes outside the boundaries. I've examined the other numbers for -box vectors and -center, but the result was the same. I don't know what to do, please help me. thank you in advanced. -zahra -- gmx-users mailing listgmx-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
