Re: [gmx-users] Fwd: Concatenating two trajectories
No, By default it will give the starting time from where it started. I doubt your simulation extension has some problem. The commands to extend a simulation are tpbconv -s old.tpr -extend time in ps -o new.tpr mdrun -v -s new.tpr -cpi state.cpt -deffnm new Hope it will help you. On Tue, Apr 22, 2014 at 11:00 AM, Sunita sunita@gmail.com wrote: Hello Venkat, Yeah, I think by default it will give 0 ps as start time for both trajectories and it should be set by user using -settime flag Correct me if I am wrong. Regards -- View this message in context: http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015992.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 120, Issue 95
Hello, Several time I have extended my jobs using the protocol you have mentioned above. I always used to get my output appended to the previous one, which never required any concatenation. This time my aim was to extend the job using new.mdp files (as the previous one contained simulated annealing protocols to reach 500K temp and the new job to have trajectories at 500K only) So, I used 1st protocol of Changing .mdp file given in http://www.gromacs.org/Documentation/How-tos/Extending_Simulations. grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt and mdrun -s new.tpr As, a result I got new files this time, creating backup files for the previous ones. I renamed those backup files as old files and trying to concatenate with the new ones. I have only one .cpt file now, as its backup file was not created. Please let me know, If I am wrong or any alternate way to do this. Regards On Tue, Apr 22, 2014 at 3:24 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Cannot write trajectory frame;maybe you are out of disk space (Andrew Bostick) 2. Re: Fwd: Concatenating two trajectories (Sunita) 3. No default U-B types (Shima Arasteh) 4. Re: Fwd: Concatenating two trajectories (Venkat Reddy) 5. deprecating the Nabble forums (Rossen Apostolov) 6. Re: negative HB lifetime (Erik Marklund) 7. Re: No default U-B types (Justin Lemkul) -- Message: 1 Date: Mon, 21 Apr 2014 19:30:32 -0700 From: Andrew Bostick andrew.bosti...@gmail.com To: gmx-users gmx-us...@gromacs.org Subject: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space Message-ID: camgms2wli3dhlumhw_erpy5tmffebcyhqenoly340nojm1q...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Dear Mark Thanks for your reply. I googled file permission in linux OS. After that I did following steps: I created a directory entitled input. I put pdb and mdp files in the input directory. I used following command to change permission: chmod -R 777 input Now I will md simulation steps (pdb2gmx editconf ..) Is my manner true? -- Message: 2 Date: Mon, 21 Apr 2014 22:30:00 -0700 (PDT) From: Sunita sunita@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fwd: Concatenating two trajectories Message-ID: 1398144600309-5015992.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Hello Venkat, Yeah, I think by default it will give 0 ps as start time for both trajectories and it should be set by user using -settime flag Correct me if I am wrong. Regards -- View this message in context: http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015992.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Message: 3 Date: Mon, 21 Apr 2014 23:31:55 -0700 (PDT) From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion List for GROMACS Users gmx-us...@gromacs.org Subject: [gmx-users] No default U-B types Message-ID: 1398148315.77320.yahoomail...@web162405.mail.bf1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi all, There is an unnatural sidechain in my input file, so I added new lines as new-defined(DPP) residue to the .rtp and .hdb files. Also there were some missed bonds, angles, and dihedrals in generated .top file, which manually added in. When I go through the grompp to do EM, I find a fatal error about the new defined residue: No default U-B types As I checked this kind of angle, it exists in other residues such as lysine as well. This angle is (defined by atom types):? CT1 CT2 NH3 I checked the atom names, It seems ok. Part of the top file is as follow: ?residue?? 1 DPP rtp DPP? q +2.0 1??? NH3? 1??? DPP? N? 1?? -0.3 14.007?? ; qtot -0.3 2 HC? 1??? DPP H1? 2?? 0.33? 1.008?? ; qtot 0.03 3 HC? 1??? DPP H2? 3?? 0.33? 1.008?? ; qtot 0.36 4 HC? 1??? DPP H3? 4?? 0.33? 1.008?? ; qtot 0.69 5??? CT1? 1??? DPP CA? 5?? 0.21 12.011?? ; qtot 0.9 6 HB? 1??? DPP HA? 6??? 0.1? 1.008?? ;
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 120, Issue 95
On 4/22/14, 7:18 AM, sunita gupta wrote: Hello, Several time I have extended my jobs using the protocol you have mentioned above. I always used to get my output appended to the previous one, which never required any concatenation. This time my aim was to extend the job using new.mdp files (as the previous one contained simulated annealing protocols to reach 500K temp and the new job to have trajectories at 500K only) So, I used 1st protocol of Changing .mdp file given in http://www.gromacs.org/Documentation/How-tos/Extending_Simulations. grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt and mdrun -s new.tpr As, a result I got new files this time, creating backup files for the previous ones. I renamed those backup files as old files and trying to concatenate with the new ones. I have only one .cpt file now, as its backup file was not created. Please let me know, If I am wrong or any alternate way to do this. If you re-run grompp, the default values of init_t and init_step are zero. If you didn't reset those values, your trajectory will start over from time = 0. If you want to concatenate the resulting output to a previous run, you should indeed reset the start time with trjcat -settime, as stated before. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Silica Nanoparticles
On 4/22/14, 11:12 AM, Kazem Sepehrinia wrote: Hi Dear All, Have any of you guys prepared silica nanoparticles in your Molecular Simulation studies? I used some open databases for obtaining of bulk amorphous silica file. But i'm not able to prepare silica nanoparticles. Once again i used materials studio glasses and made a nanoparticle but that one is not working also. Because i tried to minimize it and job failed. Any help would be greatly appreciated. You'll have to define not working and job failed in more detail. Is something crashing? Are there problems with topology generation? Using pdb2gmx to create a topology will likely be a major pain, since it is designed for (mostly) linear polymers, though g_x2top might handle it alright, provided you have written a suitable .n2t file. These are all the sorts of things we need to know to provide useful advice. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD, demux after 100 ns per replica
Hi, I did an extra modification to the *.pl with the aim of being more general with the time step. I have just added a line that asks the time step. Note: I don't know perl, so I apologize for the rustic way how I modified the file. Thanks, Andrea proof_demux.pl http://gromacs.5086.x6.nabble.com/file/n5016005/proof_demux.pl - Andrea Pérez-Villa PhD student in Physics and Chemistry of Biological Systems SISSA, Italy -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-demux-after-100-ns-per-replica-tp5015885p5016005.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Silica Nanoparticles
You may try to use special potential designed for amorphous silica: A numerical investigation of the liquid–vapor coexistence curve of silica Yves Guissani and Bertrand Guillot J. Chem. Phys. 104, 7633 (1996) On 22 April 2014 17:12, Kazem Sepehrinia ksepehri...@gmail.com wrote: Hi Dear All, Have any of you guys prepared silica nanoparticles in your Molecular Simulation studies? I used some open databases for obtaining of bulk amorphous silica file. But i'm not able to prepare silica nanoparticles. Once again i used materials studio glasses and made a nanoparticle but that one is not working also. Because i tried to minimize it and job failed. Any help would be greatly appreciated. Thanks, Kazem Sepehrinia. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Silica Nanoparticles
Dear Mehmet, Thank you for replying. -Kazem On Tue, Apr 22, 2014 at 2:07 PM, Suzen, Mehmet msu...@gmail.com wrote: You may try to use special potential designed for amorphous silica: A numerical investigation of the liquid–vapor coexistence curve of silica Yves Guissani and Bertrand Guillot J. Chem. Phys. 104, 7633 (1996) On 22 April 2014 17:12, Kazem Sepehrinia ksepehri...@gmail.com wrote: Hi Dear All, Have any of you guys prepared silica nanoparticles in your Molecular Simulation studies? I used some open databases for obtaining of bulk amorphous silica file. But i'm not able to prepare silica nanoparticles. Once again i used materials studio glasses and made a nanoparticle but that one is not working also. Because i tried to minimize it and job failed. Any help would be greatly appreciated. Thanks, Kazem Sepehrinia. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
