[gmx-users] rotate a .xtc file?
Thanks Roland, I'll give it a shot. Chris. Hi, since this is such a simple problem I suggest to simply write a program to do it. I suggest to start with either the xdrfile library or with the the template (available under share). My experience is writing those small things myself is much faster than searching the net and asking on the list. Roland On Tue, Nov 2, 2010 at 11:30 PM, chris.ne...@utoronto.ca wrote: [Hide Quoted Text] Dear users, I have 100 GB of .xtc with 3E6 total frames that that I would like to rotate by 90 deg about the z axis. For a .gro file, I could do this with editconf. trjconv does not appear to have this ability. Writing out so many frames as .gro just to rotate it with editconf and turn it back into a .xtc seems like a slow idea. trjconv -fit rotate will not work either since there is no way to predefine the angle of rotation. Does anybody have any ideas? I saw this: http://www.mail-archive.com/gmx-users@gromacs.org/msg20311.html but no reply. Thanks, Chris. -- 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] Reg:Usage of Walls
Hi all I have a question regarding the usage of walls. what for walls are used? what difference does the presence of walls make in the simulation? kindly me more specific (if possible explain it with an example). any help is highly appreciated. it will be of great use for all the new users of Gromacs. Regards Vinoth -- 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
Re: [gmx-users] Reg:walls and pbc xy
The walls are simply interactions between the atomtype of the wall you specified (in your case opls_966 and opls_968), and the rest of the system, at the planes defined by z=0 or z=z_box. wall_type= 9-3 wall_r_linpot= 1 wall_atomtype = opls_966 opls_968 wall_density= 9-3 9-3 wall_ewald_zfac= 3 There seems to be a problem with your 'wall_density' setting, though. They serve as scalar multipliers of the interaction strength, so they should be numbers. One reason things might be blowing up is if there are strong forces: when atoms are too close to the wall. Sander On Nov 3, 2010, at 06:41 , vinothkumar mohanakrishnan wrote: Hi all Can anyone help me out with the wall settings for running above mentioned liquid-liquid interface. with the mdp file i have my system is exploding. any help is highly appreciated. Regards Vinoth On Tue, Nov 2, 2010 at 3:58 PM, vinothkumar mohanakrishnan kmvin...@gmail.com wrote: Hi Berk Thank you. what settings i should change in mdp file (energy minimisation) to run the energy minimisation for the single liquid-liquid interface (liquid-vapour interface at the other two extremes) without any issues? kindly be specific ( what parameter i should change) below is my mdp file. any help is highly appreciated. integrator= steep emtol= 40.0 emstep = 0.01 nsteps= 1 nstxout= 100 nstvout= 100 nstfout= 100 nstlog= 100 nstenergy= 100 nstlist= 5 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0 vdwtype= Cut-off rvdw= 1.0 ewald_geometry= 3dc nwall= 2 wall_type= 9-3 wall_r_linpot= 1 wall_atomtype = opls_966 opls_968 wall_density= 9-3 9-3 wall_ewald_zfac= 3 pbc= xy fourierspacing = 0.18 Regards Vinoth On Tue, Nov 2, 2010 at 3:41 PM, Berk Hess g...@hotmail.com wrote: I meant to say that if you see effects of one interface on another with a layer of 1 nm thickness/height, these effects will be less with a layer of 2 nm thickness and even less with 10 nm thickness. Berk Date: Tue, 2 Nov 2010 15:30:34 +0530 Subject: Re: [gmx-users] Reg:walls and pbc xy From: kmvin...@gmail.com To: gmx-users@gromacs.org Hi Berk Thank you once again. How can i use thick layers and what is the procedure? can you explain it bit more on this? Regards Vinoth On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess g...@hotmail.com wrote: Hi, I have not heard about such issues, but it might depend a lot on your particular application. I would think you will always have disturbances, no matter if you use two interfaces, one interface with walls or one liquid-liquid interface and two liquid-vapour interfaces. The only solution to such problems is using thicker layers. The wall are on the bottom (z=0) and top (z=z_box) of the box, as the manual says. Berk Date: Tue, 2 Nov 2010 14:59:31 +0530 Subject: Re: [gmx-users] Reg:walls and pbc xy From: kmvin...@gmail.com To: gmx-users@gromacs.org Hi Berk I need only one interface because if i have two interfaces the capillary waves from one interface disturb the other even though the distance between the average positions of the two interfaces are larger than the potential cut-off (this was said in the literature). Can anyone explain me why walls are used for interfaces? and what is the purpose of using walls?. suppose if i put nwall =2 where exactly are the walls created? can anyone explain me with an example? i read the manual but it is not making any sense to me. if i know this i know what correction i should make in my mdp file to make it work for pbc xy. any help is highly appreciated. Regards Vinoth On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess g...@hotmail.com wrote: Hi, With wall_r_linpot your wall potential is linear from 1 nm downwards. Since the LJ force is negative at 1 nm, your atoms are attracted to the walls. But why not simply use two interfaces? You get double the sampling for free and you do not have to bother with complicated wall setups. Berk Date: Tue, 2 Nov 2010 11:49:48 +0530 From: kmvin...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Reg:walls and pbc xy Hi Gromacians I want to create a liquid-liquid interface and study its properties. Hence i combined two boxes ( say water and DCE). The two boxes are well equilibrated before merging and i created an interface. Now i want to perform energy minimisation for the interface by appling pbc in the xy direction and using walls. ( If i apply pbc in all the directions i get two interfaces where as i need only one interface hence i am applying it only on the xy direction and removing the boundary condition in the Z
RE: [gmx-users] Reg:walls and pbc xy
Indeed. I overlooked the strange wall_density setting in my first answer. But remember to also change wall_r_linpot. As I said, a LJ like potential that is linear from 1 nm downwards will be completely attractive and will pull all atoms to infinity. Berk From: pr...@cbr.su.se Subject: Re: [gmx-users] Reg:walls and pbc xy Date: Wed, 3 Nov 2010 09:04:23 +0100 To: gmx-users@gromacs.org The walls are simply interactions between the atomtype of the wall you specified (in your case opls_966 and opls_968), and the rest of the system, at the planes defined by z=0 or z=z_box. wall_type= 9-3 wall_r_linpot= 1 wall_atomtype = opls_966 opls_968 wall_density= 9-3 9-3 wall_ewald_zfac= 3 There seems to be a problem with your 'wall_density' setting, though. They serve as scalar multipliers of the interaction strength, so they should be numbers. One reason things might be blowing up is if there are strong forces: when atoms are too close to the wall. Sander On Nov 3, 2010, at 06:41 , vinothkumar mohanakrishnan wrote:Hi all Can anyone help me out with the wall settings for running above mentioned liquid-liquid interface. with the mdp file i have my system is exploding. any help is highly appreciated. Regards Vinoth On Tue, Nov 2, 2010 at 3:58 PM, vinothkumar mohanakrishnan kmvin...@gmail.com wrote: Hi Berk Thank you. what settings i should change in mdp file (energy minimisation) to run the energy minimisation for the single liquid-liquid interface (liquid-vapour interface at the other two extremes) without any issues? kindly be specific ( what parameter i should change) below is my mdp file. any help is highly appreciated. integrator= steep emtol= 40.0 emstep = 0.01 nsteps= 1 nstxout= 100 nstvout= 100 nstfout= 100 nstlog= 100 nstenergy= 100 nstlist= 5 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0 vdwtype= Cut-off rvdw= 1.0 ewald_geometry= 3dc nwall= 2 wall_type= 9-3 wall_r_linpot= 1 wall_atomtype = opls_966 opls_968 wall_density= 9-3 9-3 wall_ewald_zfac= 3 pbc= xy fourierspacing = 0.18 Regards Vinoth On Tue, Nov 2, 2010 at 3:41 PM, Berk Hess g...@hotmail.com wrote: I meant to say that if you see effects of one interface on another with a layer of 1 nm thickness/height, these effects will be less with a layer of 2 nm thickness and even less with 10 nm thickness. Berk Date: Tue, 2 Nov 2010 15:30:34 +0530 Subject: Re: [gmx-users] Reg:walls and pbc xy From: kmvin...@gmail.com To: gmx-users@gromacs.org Hi Berk Thank you once again. How can i use thick layers and what is the procedure? can you explain it bit more on this? Regards Vinoth On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess g...@hotmail.com wrote: Hi, I have not heard about such issues, but it might depend a lot on your particular application. I would think you will always have disturbances, no matter if you use two interfaces, one interface with walls or one liquid-liquid interface and two liquid-vapour interfaces. The only solution to such problems is using thicker layers. The wall are on the bottom (z=0) and top (z=z_box) of the box, as the manual says. Berk Date: Tue, 2 Nov 2010 14:59:31 +0530 Subject: Re: [gmx-users] Reg:walls and pbc xy From: kmvin...@gmail.com To: gmx-users@gromacs.org Hi Berk I need only one interface because if i have two interfaces the capillary waves from one interface disturb the other even though the distance between the average positions of the two interfaces are larger than the potential cut-off (this was said in the literature). Can anyone explain me why walls are used for interfaces? and what is the purpose of using walls?. suppose if i put nwall =2 where exactly are the walls created? can anyone explain me with an example? i read the manual but it is not making any sense to me. if i know this i know what correction i should make in my mdp file to make it work for pbc xy. any help is highly appreciated. Regards Vinoth On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess g...@hotmail.com wrote: Hi, With wall_r_linpot your wall potential is linear from 1 nm downwards. Since the LJ force is negative at 1 nm, your atoms are attracted to the walls. But why not simply use two interfaces? You get double the sampling for free and you do not have to bother with complicated wall setups. Berk Date: Tue, 2 Nov 2010 11:49:48 +0530 From: kmvin...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Reg:walls and pbc xy Hi Gromacians I want to create a liquid-liquid interface and study its properties. Hence i combined two boxes ( say water and DCE). The two boxes are well equilibrated before merging and i created an interface. Now i want to
[gmx-users] center peptide in simulation box
Dear Mark Abraham In March 2010, In reply to question about [center peptide in simulation box], You answered: OK, well keep playing with the trjconv options and choosing sensible groups for centering until you find something that pleases you. You may need to do two different trjconv operations - one to center the peptide and one to group the waters in the same periodic cell as the peptide. I want to know how can I do last (group the waters in the same periodic cell as the peptide)? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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] trjconv -pbc/ box/ solvent
Hi gromacs users I want to know after using trjconv -pbc, box disappears and solvent molecule recedes from solute. is it true? -- 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] trjconv -pbc/box /solvent
Dear Justin thanks for your attentions In my case, after md simulation my protein diffuse out from one side of box. for solution I used trjconv -pbc nojump. then problem fixed but box disappears and water molecules recedes from protein. -- 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
Re: [gmx-users] trjconv -pbc/box /solvent
shahab shariati wrote: Dear Justin thanks for your attentions In my case, after md simulation my protein diffuse out from one side of box. for solution I used trjconv -pbc nojump. then problem fixed but box disappears and water molecules recedes from protein. That sounds like the expected behavior. The water molecules will appear to diffuse outward instead of jumping back to the other side of the box. I generally find that trjconv -pbc mol -ur compact -center has a much better effect, for visualization purposes. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] trjconv -pbc/box /solvent
shahab shariati wrote: Dear Justin in my case only -pbc nojump fix problem. my purpose is not visualization. do this xtc file ,in which protein diffuse out from box, cause any problem in analysis? if yes, how can I fix it? This same question has come up several times within the last week or two. Please check the archives for more details, but most Gromacs tools handle PBC internally. Some tools do not (g_rms, g_gyrate, etc), requiring PBC correction. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Res: [gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?
From: Chih-Ying Lin chihying2...@gmail.com To: gmx-users@gromacs.org Sent: Quarta-feira, 3 de Novembro de 2010 0:10:47 Subject: [gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ? Hi I read some papers and many simulations were performed under high temperature to induce the unfolded protein. However, the authors did not mention how they conducted the simulations under high temperature, 498 K. They did not mention which NVT or NPT were adopted for such high temperature. None of any parameters about the temperature coupling and pressure coupling were described on the papers. Hello Lin, do you know this article? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555740/ It's simple and has a fairly detailed section of the high temperature methods. It should be a good start. Are there any standard procedures to perform High temperature - MD simulation? Where can I find the standard procedures? I think one of the main issues you have to mind in a high T MD, is the explicit solvent. It is possible to mantain the water liquid under a normal pressure even at 498K, I'll search my files for the article that reviews this stuff. What water model are you using? At 498K, protein is cooked. Under NPT, the water evaporated. = so, turn on pressure coupling with a (very) high pressure to keep the water molecules. Under NVT, the pressure increased dramatically. So, to run MD simulations under the high temperature means to run the MD simulation under high pressure at the same time? But, I did read one paper that the authors performed the MD simulation under high temperature and high pressures separately and further discuss the effect the high temperature and the high pressures on protein separately. Thank you Lin Ricardo. --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo. Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil. Phone: +55 16 36024840. Curriculum Lattes:http://lattes.cnpq.br/0777038258459931 ross_...@yahoo.com.br,rsoa...@fcfrp.usp.br -- 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
Re: [gmx-users] continue Prod run from NPT eq
Please keep all Gromacs-related correspondence on the gmx-users list, especially when digging up an old thread. See comments below. manu.mura wrote: Dear Justin, I have the same problem. I started with Berendsen during NPT and I switch the thermostat (Nose-Hoover ) to run MD. I get the following error. Program grompp_mpi_d, VERSION 4.5.1 Source code file: enxio.c, line: 1022 Fatal error: Could not find energy term named 'Xi-0-Protein' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am not able to do the checkpoint file ( grompp -t *.cpt) because I get another error. Saying that you get another error is not helpful. You cannot pass an .edr file to grompp when switching thermostats. You should be able to pass a checkpoint file to preserve all velocities, etc. If you want further help, post the exact error message, and perhaps your .mdp file. Otherwise, all I can say is either something went wrong or you're doing something wrong. -Justin Could you help me. Thank you Best Regards Manuela -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] Re: pressure of the liquid in NPT and NVT
Hi :) I suspect the volume fluctuations are not symmetric around the idealized volume at 1 bar. I think that would mean that the average volume does not correspond to the idealized volume, as you assumed. Cheers, Tsjerk On Wed, Nov 3, 2010 at 12:19 AM, Dallas Warren dallas.war...@monash.edu wrote: What is the volume fluctuation like just prior to the end of the previous run (NPT) that is used as the starting point for the NVT run? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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 -- 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 -- 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] unexpexted stop of simulation
Dear all, I'm performing a three-day simulation. It runs well for the first day, but stops for the second one. The error message is below. Does anyone know what might be the problem? Thanks Liang Program mdrun, VERSION 4.5.1-dev-20101008-e2cbc-dirty Source code file: /home/z8g/download/gromacs.head/src/gmxlib/checkpoint.c, line: 1748 Fatal error: Failed to lock: md100ns.log. Already running simulation? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sitting on a rooftop watching molecules collide (A Camp) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 32 gcq#348: Sitting on a rooftop watching molecules collide (A Camp) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- [node139:04470] [[37327,0],0]-[[37327,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) -- mpiexec has exited due to process rank 0 with PID 4471 on node node139 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpiexec (as reported here). -- 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
Re: [gmx-users] unexpexted stop of simulation
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11/03/2010 03:38 PM, Hong, Liang wrote: Dear all, I'm performing a three-day simulation. It runs well for the first day, but stops for the second one. The error message is below. Does anyone know what might be the problem? Thanks Liang Program mdrun, VERSION 4.5.1-dev-20101008-e2cbc-dirty Source code file: /home/z8g/download/gromacs.head/src/gmxlib/checkpoint.c, line: 1748 Fatal error: Failed to lock: md100ns.log. Already running simulation? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sitting on a rooftop watching molecules collide (A Camp) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 32 gcq#348: Sitting on a rooftop watching molecules collide (A Camp) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- [node139:04470] [[37327,0],0]-[[37327,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) -- mpiexec has exited due to process rank 0 with PID 4471 on node node139 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpiexec (as reported here). Perhaps the queueing system of your cluster does not allow running a job longer than 24h. Or the default is 24h and you have to supply the corresponding information to the submission script. /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzRdrEACgkQLpNNBb9GiPm1sgCg3LkRUWgiZvOOH/GIjp5ifbZI bJcAn1aamCMWlWTokD1+eDCLG1WhT/rd =4Vs3 -END PGP SIGNATURE- -- 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
Re: [gmx-users] unexpexted stop of simulation
Hi, there was also an issue with the locking of the general md.log output file which was resolved for 4.5.2. An update might help. Carsten On Nov 3, 2010, at 3:50 PM, Florian Dommert wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11/03/2010 03:38 PM, Hong, Liang wrote: Dear all, I'm performing a three-day simulation. It runs well for the first day, but stops for the second one. The error message is below. Does anyone know what might be the problem? Thanks Liang Program mdrun, VERSION 4.5.1-dev-20101008-e2cbc-dirty Source code file: /home/z8g/download/gromacs.head/src/gmxlib/checkpoint.c, line: 1748 Fatal error: Failed to lock: md100ns.log. Already running simulation? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sitting on a rooftop watching molecules collide (A Camp) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 32 gcq#348: Sitting on a rooftop watching molecules collide (A Camp) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- [node139:04470] [[37327,0],0]-[[37327,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) -- mpiexec has exited due to process rank 0 with PID 4471 on node node139 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpiexec (as reported here). Perhaps the queueing system of your cluster does not allow running a job longer than 24h. Or the default is 24h and you have to supply the corresponding information to the submission script. /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzRdrEACgkQLpNNBb9GiPm1sgCg3LkRUWgiZvOOH/GIjp5ifbZI bJcAn1aamCMWlWTokD1+eDCLG1WhT/rd =4Vs3 -END PGP SIGNATURE- -- 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 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
RE: [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2
Hi, I saw your message, but I wanted to discuss with others before answering. I have not had a chance for that yet, but I can answer anyhow. 1. This is a mistake. The person converting the original Charmm files edited his conversion script, but the special cases can not be treated with this script. We'll update them. 2. Water is always a special case. It charge group is smaller than most other charge groups and force field independent. For performance reasons we don't want to change this. (although in a future release we might get rid of the complete charge group concept) 3. Termini charge groups were also overlooked. We can fix this. I added support for charge group numbers in the tdb file some time ago. Berk Date: Wed, 3 Nov 2010 14:50:34 + From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2 Hi, I sent this message a few days ago to the list but have not had a reply. I feel some of the issues are quite important and so I am sending it again: I have a few questions/comments about the implementation of the single atom charge groups with the CHARMM27 force field that maybe someone can help with: 1. There are some entries in aminoacids.rtp which have not been converted to having every atom in a separate charge group (ASPP, CYS2, GLUP, LSN, HEME, HEO2, O2, C2 and HOH, hopefully I didn't miss any!). I understand these are some of the less commonly used entries, have they been left out for a reason? By the way I also noticed during a quick test for this that there is not an rtp entry for ARGN but it is given as an option by pdb2gmx when using -inter. 2. Relating to 1 are the charge groups in the water models, which have also been left as a water in a single charge group. I think I remember reading somewhere that this is needed for the fast water loops in GROMACS, so I assume this has been done on purpose. My concern is that this is different to the TIP3P and TP3M entries in the aminoacids.rtp file. If this has been done on purpose for the water models, then maybe TIP3 and TP3M should also just have one charge group (as in the HOH entry)? 3. Finally, another concern I have is that when adding termini to a protein (from aminoacids.c.tdb and aminoacids.n.tdb) then the terminal atoms are still added as one charge group by pdb2gmx. I am not sure of a way around this, apart from still using the -nochargegrp option, or having AMBER forcefield style rtp entries for the N and C terminal residues (undesirable I am sure). Cheers Tom On 30/10/10 20:56, Rossen Apostolov wrote: Dear Gromacs users and developers, A new bugfix release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz. Here is a list of some of the resolved issues for 4.5.1: * CHARMM force field now has single atom charge groups (pdb2gmx -nochargegrp no longer required) * Made pdb2gmx -chainsep option work * Fixed possible inconvenient npme node choice with pme load between 0.33 and 0.50 which could lead to very slow mdrun performance. * Made Generalized Born gb_algorithm and sa_surface_tension active and added a separate non-polar solvation term to the output. * Fixed issues in Generalized Born code that could cause incorrect results with SSE and all-vs-all inner-loops. * Fixed bug with pressure coupling with nstlist=-1 that resulted in extremely low densities. * Fixed corrupted energy and checkpoint file output with BAR free energy calculations. * Fixed normalization of g_density using only the last frame. * Fixed several issues with cmake * Several minor fixes. Once again big thanks to all developers for their hard work, and to all users for their contributions! Happy simulating! Rossen -- Dr Thomas Piggot University of Southampton, UK. -- 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 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
RE: [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2
I forgot to say that for the water models the rtp entries are only used to recognize the atoms. For the topology the itp files in the .ff dir are used. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2 Date: Wed, 3 Nov 2010 20:32:58 +0100 Hi, I saw your message, but I wanted to discuss with others before answering. I have not had a chance for that yet, but I can answer anyhow. 1. This is a mistake. The person converting the original Charmm files edited his conversion script, but the special cases can not be treated with this script. We'll update them. 2. Water is always a special case. It charge group is smaller than most other charge groups and force field independent. For performance reasons we don't want to change this. (although in a future release we might get rid of the complete charge group concept) 3. Termini charge groups were also overlooked. We can fix this. I added support for charge group numbers in the tdb file some time ago. Berk Date: Wed, 3 Nov 2010 14:50:34 + From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2 Hi, I sent this message a few days ago to the list but have not had a reply. I feel some of the issues are quite important and so I am sending it again: I have a few questions/comments about the implementation of the single atom charge groups with the CHARMM27 force field that maybe someone can help with: 1. There are some entries in aminoacids.rtp which have not been converted to having every atom in a separate charge group (ASPP, CYS2, GLUP, LSN, HEME, HEO2, O2, C2 and HOH, hopefully I didn't miss any!). I understand these are some of the less commonly used entries, have they been left out for a reason? By the way I also noticed during a quick test for this that there is not an rtp entry for ARGN but it is given as an option by pdb2gmx when using -inter. 2. Relating to 1 are the charge groups in the water models, which have also been left as a water in a single charge group. I think I remember reading somewhere that this is needed for the fast water loops in GROMACS, so I assume this has been done on purpose. My concern is that this is different to the TIP3P and TP3M entries in the aminoacids.rtp file. If this has been done on purpose for the water models, then maybe TIP3 and TP3M should also just have one charge group (as in the HOH entry)? 3. Finally, another concern I have is that when adding termini to a protein (from aminoacids.c.tdb and aminoacids.n.tdb) then the terminal atoms are still added as one charge group by pdb2gmx. I am not sure of a way around this, apart from still using the -nochargegrp option, or having AMBER forcefield style rtp entries for the N and C terminal residues (undesirable I am sure). Cheers Tom On 30/10/10 20:56, Rossen Apostolov wrote: Dear Gromacs users and developers, A new bugfix release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz. Here is a list of some of the resolved issues for 4.5.1: * CHARMM force field now has single atom charge groups (pdb2gmx -nochargegrp no longer required) * Made pdb2gmx -chainsep option work * Fixed possible inconvenient npme node choice with pme load between 0.33 and 0.50 which could lead to very slow mdrun performance. * Made Generalized Born gb_algorithm and sa_surface_tension active and added a separate non-polar solvation term to the output. * Fixed issues in Generalized Born code that could cause incorrect results with SSE and all-vs-all inner-loops. * Fixed bug with pressure coupling with nstlist=-1 that resulted in extremely low densities. * Fixed corrupted energy and checkpoint file output with BAR free energy calculations. * Fixed normalization of g_density using only the last frame. * Fixed several issues with cmake * Several minor fixes. Once again big thanks to all developers for their hard work, and to all users for their contributions! Happy simulating! Rossen -- Dr Thomas Piggot University of Southampton, UK. -- 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 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
Re: [gmx-users] Replica exchange with scaled topology files
On 4/11/2010 1:53 AM, Sai Pooja wrote: Hi, I am running a the gromacs Replica exchange (NVT). However along with the temperatures, I have also scaled a few paramters in the topology file for each of the replicas for generating the .tpr files. Everything seems to be running fine but is this a valid thing to do? Or would gromacs simply ignore those differences? mdrun does whatever the .tpr and command line options tell it. mdrun knows about nothing (e.g. the forcefield files) that would permit it recognize a difference. Even if it could recognize such, silently doing something else would be the way madness lies... grompp is pretty good at noticing things that might be astray and giving suitable feedback. Mark -- 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
Re: [gmx-users] center peptide in simulation box
On 3/11/2010 9:04 PM, leila karami wrote: Dear Mark Abraham In March 2010, In reply to question about [center peptide in simulation box], You answered: OK, well keep playing with the trjconv options and choosing sensible groups for centering until you find something that pleases you. You may need to do two different trjconv operations - one to center the peptide and one to group the waters in the same periodic cell as the peptide. I want to know how can I do last (group the waters in the same periodic cell as the peptide)? I'd find the answer to this by reading trjconv -h and experimenting :-) Mark -- 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] About simulating lipid bi-continuous cubic phase
Dear users, I am attempting to simulate lipid cubic phase using Coarse grained MD from the spontaneous aggregation approach, starting from random mixture of lipids in solution, in the spirit of JACS 2009 paper from the Martini community. I had several technical issues before setting up the simulations and I would appreciate expert opinion on these. My main concern is about the interplay between the number of lipids in the system, initial size of the simulation cell and the pressure coupling method to use. What should be the recipe for choosing the initial number of lipids? Obviously, I would think that one has to choose the number large enough to form at least one unit cell of the bi-continuous cubic phase. But what happens if I don't choose exactly this magic number, but slightly more? Then I would think that after running the simulation, the simulation box would contain more than just a unit cell of the cubic phase. Can this be a problem? Also does the initial size of the simulation box matter if one simulates spontaneous aggregation process as long as the molecules initially fit into the box? And finally, what role should isotropic vs anisotropic pressure coupling play in such approach? Which pressure coupling method should be preferred in such spontaneous aggregation simulation? Any advice will be greatly appreciated! Thank you in advance, Sincerely, George -- 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
RE: [gmx-users] About simulating lipid bi-continuous cubic phase
George, I am attempting to simulate lipid cubic phase using Coarse grained MD from the spontaneous aggregation approach, starting from random mixture of lipids in solution, in the spirit of JACS 2009 paper from the Martini community. I had several technical issues before setting up the simulations and I would appreciate expert opinion on these. I can't comment in terms of the coarse grain type of MD, as we are performing united atom simulations of phase behaviour, but the principles are still the same. My main concern is about the interplay between the number of lipids in the system, initial size of the simulation cell and the pressure coupling method to use. What should be the recipe for choosing the initial number of lipids? Obviously, I would think that one has to choose the number large enough to form at least one unit cell of the bi-continuous cubic phase. But what happens if I don't choose exactly this magic number, but slightly more? Then I would think that after running the simulation, the simulation box would contain more than just a unit cell of the cubic phase. Can this be a problem? It is good that you are concerned, as it does influence the result. If you have sufficient size / number of molecules to form a non-integer number of unit cells, then the final structure will be distorted from what you would expect as the end result. The only way to get beyond this is have the system large enough that it is not an issue, and computational speeds are not at this level as of yet. You have a number of options available. Put in the correct number or dimensions, but you are constraining the results of the simulation, you might as well preassemble it, since you aren't actually allowing it to spontaneously form a structure, you are guiding it. Acknowledge that the structure formed may not be perfect and will have flaws in it, due to the dimensional issue, and simply work that into your work. Also does the initial size of the simulation box matter if one simulates spontaneous aggregation process as long as the molecules initially fit into the box? If you are going for spontaneous aggregation, then random distribution of the molecules within the box is what you should be starting from. And finally, what role should isotropic vs anisotropic pressure coupling play in such approach? Which pressure coupling method should be preferred in such spontaneous aggregation simulation? We played with this for quite some time. In a perfect world, it would be best to using anisotropic pressure coupling, so you do not constrain the structure that is formed. However, in the world of MDS, it is simply not possible. You encounter major issues with simulation stability, the way the pressure coupling and alternating charges across one dimension of the box interact means that eventually you will end up with the box distorting to the point that you end up with a match stick or a pancake. We even played with adding various tweaks to the coupling algorithms that increase the resistance to changes in the box dimensions as they deviate from cube or get too close to the point at which it will explode. The algorithms works great. But you get back to the same point again, ultimately you are constraining the end result. And the flow on effects of that are harder to quantify than simply staying with isotropic. We are putting together a publication on the phase behaviour stuff we have done, some mention will be made of these issues in that. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] extending simulation without cpt file
Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? Thanks, Greg -- 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
Re: [gmx-users] extending simulation without cpt file
Yongchul Chung wrote: Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? There is no bug here. You're using tpbconv wrong. If you don't provide it the .trr and .edr files corresponding to the last time frame, you're going to end up with a .tpr file that contains the full run time, instead of picking up from the last frame, since tpbconv has no knowledge that it exists. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_3.3.3_and_Before If you tell tpbconv to extend a simulation by 102000 ps with no other information, it assumes you're starting from 0. -Justin Thanks, Greg -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] extending simulation without cpt file
- Original Message - From: Yongchul Chung yxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS users gmx-users@gromacs.org Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint. Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr. Mark -- 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
Re: [gmx-users] extending simulation without cpt file
- Original Message - From: Mark Abraham mark.abra...@anu.edu.au Date: Thursday, November 4, 2010 10:38 Subject: Re: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS users gmx-users@gromacs.org - Original Message - From: Yongchul Chung yxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS users gmx-users@gromacs.org Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint. Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr. Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I used it, I'd forgotten :-) Mark -- 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
Re: [gmx-users] extending simulation without cpt file
Thanks Justin! it works now. Greg On Wed, Nov 3, 2010 at 7:39 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Mark Abraham mark.abra...@anu.edu.au Date: Thursday, November 4, 2010 10:38 Subject: Re: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS users gmx-users@gromacs.org - Original Message - From: Yongchul Chung yxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS users gmx-users@gromacs.org Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint. Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr. Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I used it, I'd forgotten :-) Mark -- 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 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
Re: [gmx-users] unexpexted stop of simulation
Hi, the reason turned out to be that the lock daemon (lockd) on the NFS server was hanging. The error could be found by dmesg. BTW: Is it somehow possible to print the kernel error messages that are shown by dmesg to the user from within GROMACS? That would help the user to directly see the reason of the error. Thus I'm looking for a function similar to strerror but which returns the kernel message not just the message of the error code (which in this case was just Input/Output errror. Roland On Wed, Nov 3, 2010 at 12:05 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, there was also an issue with the locking of the general md.log output file which was resolved for 4.5.2. An update might help. Carsten On Nov 3, 2010, at 3:50 PM, Florian Dommert wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11/03/2010 03:38 PM, Hong, Liang wrote: Dear all, I'm performing a three-day simulation. It runs well for the first day, but stops for the second one. The error message is below. Does anyone know what might be the problem? Thanks Liang Program mdrun, VERSION 4.5.1-dev-20101008-e2cbc-dirty Source code file: /home/z8g/download/gromacs.head/src/gmxlib/checkpoint.c, line: 1748 Fatal error: Failed to lock: md100ns.log. Already running simulation? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sitting on a rooftop watching molecules collide (A Camp) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 32 gcq#348: Sitting on a rooftop watching molecules collide (A Camp) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- [node139:04470] [[37327,0],0]-[[37327,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) -- mpiexec has exited due to process rank 0 with PID 4471 on node node139 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpiexec (as reported here). Perhaps the queueing system of your cluster does not allow running a job longer than 24h. Or the default is 24h and you have to supply the corresponding information to the submission script. /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzRdrEACgkQLpNNBb9GiPm1sgCg3LkRUWgiZvOOH/GIjp5ifbZI bJcAn1aamCMWlWTokD1+eDCLG1WhT/rd =4Vs3 -END PGP SIGNATURE- -- 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 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] editconf
Hi, when I choose different box types and draw them by Pymol, I see no visual difference between them. At least cubic must be different from the others. What is the reason for this? best wishes -- 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] charmm27 force filed bug for MET residue with vsites in gromacs 4.5.2
Dear all: I used gromacs 4.5.2 to generate the topology for a small protein with charmm27. pdb2gmx_mpi -f 1PIN.pdb -o protein.gro -vsite hydrogen -his -ignh -ter -p topol -nochargegrp When I try to use the topology in grompp, the following error appeared: Fatal error: Can't do GB electrostatics; the forcefield is missing 1 values for atomtype radii, or they might be negative I was able to isolate the atom that's causing the problem, which is MCH3S in the Met residue (as shown in the attached segment of the topology). It was named MCH3 as in gromacs 4.5.1. However, if I rename the atom, then another error occurs: No default Constr. No Conn. types (between atom 181 and 182) This problem does NOT show up in 4.5.1. Thanks, Bin 171NH1 15MET N171 -0.47 15.015 ; qtot 1.53 172 H 15MET HN172 0.31 0 ; qtot 1.84 173CT1 15MET CA173 0.07 13.019 ; qtot 1.91 174 HB 15MET HA174 0.09 0 ; qtot 2 175CT2 15MET CB175 -0.18 14.027 ; qtot 1.82 176 HA 15METHB1176 0.09 0 ; qtot 1.91 177 HA 15METHB2177 0.09 0 ; qtot 2 178CT2 15MET CG178 -0.14 14.027 ; qtot 1.86 179 HA 15METHG1179 0.09 0 ; qtot 1.95 180 HA 15METHG2180 0.09 0 ; qtot 2.04 181 S 15MET SD181 -0.09 32.06 ; qtot 1.95 182 MCH3S 15MET MCE1182 0 7.5175 ; qtot 1.95 183 MCH3S 15MET MCE2183 0 7.5175 ; qtot 1.95 184CT3 15MET CE184 -0.22 0 ; qtot 1.73 185 HA 15METHE1185 0.09 0 ; qtot 1.82 186 HA 15METHE2186 0.09 0 ; qtot 1.91 187 HA 15METHE3187 0.09 0 ; qtot 2 188 C 15MET C188 0.51 12.011 ; qtot 2.51 189 O 15MET O189 -0.51 15.999 ; qtot 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/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
Re: [gmx-users] editconf
Hi Mustafa, Check the section on periodic boundary conditions in the manual. Also be sure to use 'show cell' in Pymol to display the triclinic unit cell. That will show you the differences. Besides that, do a direct comparison of the lines encoding the boxes; either the last line of a .gro fil, or the line starting with 'CRYST1' in a.pdb file. Cheers, Tsjerk On Thu, Nov 4, 2010 at 1:23 AM, mustafa bilsel mfbil...@gmail.com wrote: Hi, when I choose different box types and draw them by Pymol, I see no visual difference between them. At least cubic must be different from the others. What is the reason for this? best wishes -- 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/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 -- 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 -- 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
