[gmx-users] diffusion coefficient
Hi Everyone, I have been trying to calculate diffusion coefficient for water. I am trying to reproduce the numbers published in journal papers. I am using SPCE water model. I use the g_msd analysis tool. g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8 I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I equilibriate the system for a ns and then run for additional 10 ps for analysis. Here are some of the numbers that i get a. With Berendsen's T coupling and P coupling on i get 4.4941 (+/- 0.2992) 1e-5 cm^2/s b. With Berendsen's T coupling on and P coupling off I get 3.2469 (+/- 0.1076) 1e-5 cm^2/s c. With Berendsen's T coupling on and P coupling off for 1ns and then T,P coupling both off (for analysis part) i get 2.8085 (+/- 0.0310) 1e-5 cm^2/s . c is closest to the widely accepted experimental value of 2.3 1e-5 cm^2/s but its not quite right. Could someone explain to me why the values obtained in above 3 cases are widely different and may be give some tips about the right procedure to calculate diffusion (method and invoking the g_msd tool)? Thank you Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: saving the protein conformation after 10ps simulation
Hi all, I am trying to save the conformation of my protein after 10ps simulation .. I am getting the following error :- Software inconsistency error: Not supported in write_sto_conf Can anybody tell me how to fix this error .. -- Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics Pondicherry University Puducherry India Mob. +919962670525 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] diffusion coefficient
Hi, you already have your solution at hand. On 10.02.2010, at 10:05, Amit Choubey wrote: Hi Everyone, I have been trying to calculate diffusion coefficient for water. I am trying to reproduce the numbers published in journal papers. I am using SPCE water model. I use the g_msd analysis tool. g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8 I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I equilibriate the system for a ns and then run for additional 10 ps for analysis. Here are some of the numbers that i get a. With Berendsen's T coupling and P coupling on i get 4.4941 (+/- 0.2992) 1e-5 cm^2/s b. With Berendsen's T coupling on and P coupling off I get 3.2469 (+/- 0.1076) 1e-5 cm^2/s c. With Berendsen's T coupling on and P coupling off for 1ns and then T,P coupling both off (for analysis part) i get 2.8085 (+/- 0.0310) 1e-5 cm^2/s . c is closest to the widely accepted experimental value of 2.3 1e-5 cm^2/s but its not quite right. You obtain a quite good estimation of the diffusion coefficient when not applying the Berendsen coupling scheme. The reason for this is that Berendsen coupling does not allow to generate a correct thermodynamic ensemble. Applying v-rescale or Nose-Hoover in combination with Parrinello-Rahman should yield more accurate results, because the take the way of sampling the phase space in an appropriate manner into account. Cheers, Flo Could someone explain to me why the values obtained in above 3 cases are widely different and may be give some tips about the right procedure to calculate diffusion (method and invoking the g_msd tool)? Thank you Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 PGP.sig Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: saving the protein conformation after 10ps simulation
bharat gupta wrote: Hi all, I am trying to save the conformation of my protein after 10ps simulation .. I am getting the following error :- Software inconsistency error: Not supported in write_sto_conf Can anybody tell me how to fix this error .. Not without more information, like the Gromacs version you're using and what the exact command was that gave this error. Looks like you may have a version incompatibility (i.e., mixing versions between prep/simulation/analysis). -Justin -- Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics Pondicherry University Puducherry India Mob. +919962670525 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] REMD demux problem.
Hi all, I met a problem when I try to use trjcat to connect the trajectory files of REMD. I used 16 replicas for my simulation, and used demux.pl perl script to generate the replica_index.xvg and replica_temp.xvg. Then I used trjcat -f xtc_*.xtc -demux replica_index.avg, however got an error information as below: Reading frame 0 time0.000 Segmentation fault Then when I tried trjcat -f traj*.trr -o traj.trr -demux replica_index.xvg, got another error as this: Fatal error: You have specified 17 files and 16 entries in the demux table Can anyone give me some advice on what have gone wrong? Thanks a lot. _ 您的电子邮件和更灵活的即时通信。免费获取 Windows Live Hotmail。 https://signup.live.com/signup.aspx?id=60969-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology
tekle...@ualberta.ca wrote: Dear Justin, First of all thank you for your help.. I have developed the toplogy file for my molecule using the PRODRG server. But the topology did not include properly the carboxylic acid functional group ( with proton) instead the software assumes both oxygens as identical due to resonance. Therefore I want to modify my topology .what do I need to do. From the PRODRG FAQ: Q: PRODRG doesn't properly protonate my molecule. A: This can be fixed by adding the command ADDHYD atomname or DELHYD atomname to your input drawing/PDB file. No need to hack the topology. Run PRODRG once to identify which atom name it will assign to the oxygens, then follow the instructions above. -Justin In side my topology (initial) === 44 CH1 1 UNK CA130.14313.0190 45 C 1 UNK C 130.37212.0110 46 OM 1 UNK OXT 13-0.757 15.9994 47 OM 1 UNK O 13-0.758 15.9994 MODIFIED to the following topology 44 CH1 1 UNK CA13 XXX 13.0190 45 C 1 UNK C 13 XXX 12.0110 46 O 1 UNK OXT 13 XXX 15.9994 47 OA 1 UNK O 13 XXX 15.9994 48 HO 1 UNK HAA 13 XXX 1.00800 === XXX refers to a charge of each .. How can I allocate a charge distribution for each united atom molecule in the modified topology ... Remark I checked the .RTP file and I have found the following information for the [ ASPH] residue CG C 0.53000 2 OD1 O-0.38000 2 OD2OA-0.54800 2 HD2HO 0.39800 2 But in this case eventhough this describes for the carboxilic acid functional group . It does not include CH1 in the same group.. what do I need to do to Example CA CH1 XXX 2 CG C 0.53000 2 OD1 O-0.38000 2 OD2OA-0.54800 2 HD2HO 0.39800 2 XX is the new charge for CH1 which I do not know. can you help. or simply I have to put 0.0 have a great day Rob *** The entire Topology is the following ; nr type resnr resid atom cgnr charge mass 1 CH3 1 UNK CAZ 10.000 15.0350 2 CH2 1 UNK CAK 10.000 14.0270 3 CH2 1 UNK CBS 20.000 14.0270 4 CH2 1 UNK CBL 20.000 14.0270 5 CH2 1 UNK CBG 30.000 14.0270 6 CH2 1 UNK CBM 30.000 14.0270 7 CH1 1 UNK CBA 30.000 13.0190 8 CH2 1 UNK CBD 30.000 14.0270 9 CH2 1 UNK CBE 30.000 14.0270 10 CH2 1 UNK CBF 40.000 14.0270 11 CH2 1 UNK CBJ 40.000 14.0270 12 CH2 1 UNK CBN 50.101 14.0270 13 CH3 1 UNK CBT 50.057 15.0350 14 NR6* 1 UNK NBU 50.069 14.0067 15CB 1 UNK CBP 50.346 12.0110 16 O 1 UNK OCB 5 -0.573 15.9994 17CB 1 UNK CAG 60.351 12.0110 18 O 1 UNK OCA 6 -0.565 15.9994 19 CH1 1 UNK CBI 60.178 13.0190 20 CR61 1 UNK CBO 60.018 13.0190 21 CR61 1 UNK CAV 60.018 13.0190 22CB 1 UNK CAN 70.000 12.0110 23CB 1 UNK CAR 70.000 12.0110 24CB 1 UNK CAX 80.000 12.0110 25CB 1 UNK CBC 80.000 12.0110 26 CR61 1 UNK CBH 80.000 13.0190 27 CR61 1 UNK CAW 80.000 13.0190 28 CH1 1 UNK CAQ 90.074 13.0190 29CB 1 UNK CAM 90.001 12.0110 30 CR61 1 UNK CAU 9 -0.037 13.0190 31 CR61 1 UNK CAI 9 -0.038 13.0190 32CB 1 UNK CAC100.003 12.0110 33CB 1 UNK CAE100.442 12.0110 34 O 1 UNK OBX10 -0.448 15.9994 35CB 1 UNK CAB100.003 12.0110 36CB 1 UNK CAF110.004 12.0110 37CB 1 UNK CAJ110.004 12.0110 38 CR61 1 UNK CAP11 -0.008 13.0190 39 CR61 1 UNK CAH12 -0.013 13.0190 40CB 1 UNK CAA120.003 12.0110 41CB 1 UNK CAD120.411 12.0110 42 O 1 UNK OBW12 -0.483 15.9994 43 NR6* 1 UNK N120.082 14.0067 44 CH1
Re: [gmx-users] diffusion coefficient
10 ps is too short of a trajectory, even for such a large system (for pure water it is considered large). i would guess that it is a typing-error and you ran for 10 ns? omer. On Wed, Feb 10, 2010 at 11:05, Amit Choubey kgp.a...@gmail.com wrote: I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I equilibriate the system for a ns and then run for additional 10 ps for analysis. Here are some of the numbers that i get -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] REMD demux problem.
zuole wrote: Hi all, I met a problem when I try to use trjcat to connect the trajectory files of REMD. I used 16 replicas for my simulation, and used demux.pl perl script to generate the replica_index.xvg and replica_temp.xvg. Then I used trjcat -f xtc_*.xtc -demux replica_index.avg, however got an error information as below: Reading frame 0 time0.000 Segmentation fault Then when I tried trjcat -f traj*.trr -o traj.trr -demux replica_index.xvg, got another error as this: Fatal error: You have specified 17 files and 16 entries in the demux table Can anyone give me some advice on what have gone wrong? Thanks a lot. If you have 17 input files, you need to have 17 demuxed output trajectories. Either specify 17 file names, or leave off the -o option and Gromacs will do it for you. -Justin 您的电子邮件和更灵活的即时通信。免费获取 Windows Live Hotmail。 立即注 册。 https://signup.live.com/signup.aspx?id=60969 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compilation problems orte error
Sorry for the delay in replying back. I start the job using the following script file: #$ -S /bin/bash #$ -l h_rt=47:59:00 #$ -j y #$ -pe mpich2 8 #$ -cwd cd /home/jwillia4/GRO/gromacs-4.0.7/JJW_003/PH_TORUN /home/jwillia4/GRO/bin/mpirun -np 8 /home/jwillia4/GRO/bin/mdrun_mpi -v -s md.tpr The strange thing is that sometimes it works and the job runs to completion and sometimes it crashes immediately with the orte error so I know that it is not the input files causing the problems. It seems entirely random. Has it to do with the -pe mpich2 8 line? I was previously using Open MPI installed on the cluster for common use but now have downloaded everything into my home directory. The script has been adapted from the time when I didn't have my own OpenMPI in my home directory. Perhaps it needs further alteration but I don't know what. How would I do about checking whether MPI is running? If you spot anything suspicious in the above commands please let me know. Thanks Jenny Quoting Chandan Choudhury iitd...@gmail.com: As Justin said give the command line options for mdrun and also check that your mpi environment is running. Better to run a parallel job and check its output. Chadnan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jennifer Williams wrote: Dear All, I am having problems compiling gromacs 4.0.7 in parallel. I am following the Quick and Dirty Installation instructions on the gromacs webpage. I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 following these instructions. Everything seems to compile OK and I get all the serial executables including mdrun written to my bin directory and they seem to run fine. However when I try to run mdrun_mpi on 6 nodes I get the following: [vlxbig16:08666] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08667] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08700] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08670] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08681] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08659] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_rml_base_select failed -- Returned value -13 instead of ORTE_SUCCESS Does anyone have any idea what is causing this? Computer support at my University is not sure. How are you launching mdrun_mpi (command line)? -Justin Thanks -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compilation problems orte error
On 02/10/10, Jennifer Williams jennifer.willi...@ed.ac.uk wrote:Sorry for the delay in replying back. I start the job using the following script file:#$ -S /bin/bash#$ -l h_rt=47:59:00#$ -j y#$ -pe mpich2 8#$ -cwdcd /home/jwillia4/GRO/gromacs-4.0.7/JJW_003/PH_TORUN/home/jwillia4/GRO/bin/mpirun -np 8 /home/jwillia4/GRO/bin/mdrun_mpi -v -s md.tprThe strange thing is that sometimes it works and the job runs to completion and sometimes it crashes immediately with the orte error so I know that it is not the input files causing the problems. It seems entirely random.That sounds like some kind of dynamic linking problem. You may be able to constrain the GROMACS configure program to link statically to your choice of MPI library with --enable-static or something - but only if static versions of the MPI libraries exist.Has it to do with the -pe mpich2 8 line? I was previously using Open MPI installed on the cluster for common use but now have downloaded everything into my home directory. The script has been adapted from the time when I didn't have my own OpenMPI in my home directory. Perhaps it needs further alteration but I don't know what.Try things and see. We've no idea what your queueing flags are or should be doing, but involving two different MPI libraries is asking for trouble.How would I do about checking whether MPI is running?By running a test program. Either get a Hello world program from an MPI tutorial, or perhaps something available with the library itself.MarkIf you spot anything suspicious in the above commands please let me know.ThanksJennyQuoting Chandan Choudhury iitd...@gmail.com:As Justin said give the command line options for mdrun and also check thatyour mpi environment is running. Better to run a parallel job and check itsoutput.Chadnan--Chandan kumar ChoudhuryNCL, PuneINDIAOn Mon, Feb 8, 2010 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:Jennifer Williams wrote:Dear All,I am having problems compiling gromacs 4.0.7 in parallel. I am followingtheQuick and Dirty Installation instructions on the gromacs webpage.I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 followingthese instructions.Everything seems to compile OK and I get all the serial executablesincluding mdrun written to my bin directory and they seem to run fine.However when I try to run mdrun_mpi on 6 nodes I get the following:[vlxbig16:08666] [NO-NAME] ORTE_ERROR_LOG: Not found in fileruntime/orte_init_stage1.c at line 182[vlxbig16:08667] [NO-NAME] ORTE_ERROR_LOG: Not found in fileruntime/orte_init_stage1.c at line 182[vlxbig16:08700] [NO-NAME] ORTE_ERROR_LOG: Not found in fileruntime/orte_init_stage1.c at line 182[vlxbig16:08670] [NO-NAME] ORTE_ERROR_LOG: Not found in fileruntime/orte_init_stage1.c at line 182[vlxbig16:08681] [NO-NAME] ORTE_ERROR_LOG: Not found in fileruntime/orte_init_stage1.c at line 182[vlxbig16:08659] [NO-NAME] ORTE_ERROR_LOG: Not found in fileruntime/orte_init_stage1.c at line 182--It looks like orte_init failed for some reason; your parallel process islikely to abort. There are many reasons that a parallel process canfail during orte_init; some of which are due to configuration orenvironment problems. This failure appears to be an internal failure;here's some additional information (which may only be relevant to anOpen MPI developer): orte_rml_base_select failed -- Returned value -13 instead of ORTE_SUCCESSDoes anyone have any idea what is causing this? Computer support at myUniversity is not sure.How are you launching mdrun_mpi (command line)?-JustinThanks--Justin A. LemkulPh.D. CandidateICTAS Doctoral ScholarMILES-IGERT TraineeDepartment of BiochemistryVirginia TechBlacksburg, VAjalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin--gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interfaceor send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/mailing_lists/users.phpDr. Jennifer WilliamsInstitute for Materials and ProcessesSchool of EngineeringUniversity of EdinburghSanderson BuildingThe King's BuildingsMayfield RoadEdinburgh, EH9 3JL, United KingdomPhone: ++44 (0)131 650 4 861-- The University of Edinburgh is a charitable body, registered inScotland, with registration number SC005336.-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list
[gmx-users] Re: Minimum simulation time needed to have a completely minimized structure
Hi all I wanna know that for how long shall I run the energy minimization step to minimize my modelled protein structure .. and what all parameters shall I look for the minimized structure - rms , rmsf , potential , g_energy . In g_energy total energy and potential both have to be checked ... -- Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics Pondicherry University Puducherry India Mob. +919962670525 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Minimum simulation time needed to have a completely minimized structure
bharat gupta wrote: Hi all I wanna know that for how long shall I run the energy minimization step to minimize my modelled protein structure .. and what all parameters shall I look for the minimized structure - rms , rmsf , potential , g_energy . In g_energy total energy and potential both have to be checked ... You probably won't get much in the way of RMSD or RMSF during EM; the structure shouldn't be changing drastically. Convergence of EM is usually judged based on the magnitude of Fmax and the potential (printed by mdrun at the end of EM). There is no total energy term during EM. Since there is no kinetic energy, the total energy and potential energy are the same. If you run g_energy on the .edr file, you'll see for yourself :) -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs 4.0.7 compilation problem
Hi , I want to install gromacs 4.0.7 in double precision in a 64 bit Mac computer with 8 nodes. I got the lam7.1.4 source code files and installed them using the following commands ./configure --without-fc ( it was giving an error for the fortran compiler) make make install then I get the gromacs 4.0.7 source code files and installed it as ./configure --disable-float make make install After that I try get the mpi version for mdrun make clean ./configure --enable-mpi --disable-nice --program-suffix=_mpi make mdrun I GET ERROR IN THIS STEP , With error message undefined symbols: _lam_mpi_double, referenced from: _gmx_sumd_sim in libgmx_mpi.a(network.o) _gmx_sumd in libgmx_mpi.a(network.o) _gmx_sumd in libgmx_mpi.a(network.o) _wallcycle_sum in libmd_mpi.a(gmx_wallcycle.o) _lam_mpi_byte, referenced from: _exchange_rvecs in repl_ex.o _replica_exchange in repl_ex.o _replica_exchange in repl_ex.o _replica_exchange in repl_ex.o _finish_run in libmd_mpi.a(sim_util.o) _dd_collect_vec in libmd_mpi.a(domdec.o) _dd_collect_vec in libmd_mpi.a(domdec.o) _set_dd_cell_sizes in libmd_mpi.a(domdec.o) _dd_distribute_vec in libmd_mpi.a(domdec.o) _dd_distribute_vec in libmd_mpi.a(domdec.o) _dd_partition_system in libmd_mpi.a(domdec.o) _partdec_init_local_state in libmd_mpi.a(partdec.o) _partdec_init_local_state in libmd_mpi.a(partdec.o) _gmx_rx in libmd_mpi.a(partdec.o) _gmx_tx in libmd_mpi.a(partdec.o) _gmx_bcast_sim in libgmx_mpi.a(network.o) _gmx_bcast in libgmx_mpi.a(network.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _write_traj in libmd_mpi.a(stat.o) _write_traj in libmd_mpi.a(stat.o) _gmx_pme_receive_f in libmd_mpi.a(pme_pp.o) _gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_send_force_vir_ener in libmd_mpi.a(pme_pp.o) _gmx_pme_send_force_vir_ener in libmd_mpi.a(pme_pp.o) _gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o) _dd_gatherv in libmd_mpi.a(domdec_network.o) _dd_scatterv in libmd_mpi.a(domdec_network.o) _dd_gather in libmd_mpi.a(domdec_network.o) _dd_scatter in libmd_mpi.a(domdec_network.o) _dd_bcastc in libmd_mpi.a(domdec_network.o) _dd_bcast in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv_int in libmd_mpi.a(domdec_network.o) _dd_sendrecv_int in libmd_mpi.a(domdec_network.o) _dd_sendrecv_int in libmd_mpi.a(domdec_network.o) _lam_mpi_prod, referenced from: _gprod in do_gct.o _do_coupling in do_gct.o _do_coupling in do_gct.o _do_coupling in do_gct.o _lam_mpi_float, referenced from: _gprod in do_gct.o _do_coupling in do_gct.o _do_coupling in do_gct.o _do_coupling in do_gct.o _gmx_tx_rx_real in libmd_mpi.a(partdec.o) _gmx_sumf_sim in libgmx_mpi.a(network.o) _gmx_sumf in libgmx_mpi.a(network.o) _gmx_sumf in libgmx_mpi.a(network.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _pmeredist in libmd_mpi.a(pme.o) _gmx_pme_init in libmd_mpi.a(pme.o) _gmx_sum_qgrid in libmd_mpi.a(pme.o) _gmx_sum_qgrid in libmd_mpi.a(pme.o) _gmx_parallel_transpose_xy in libmd_mpi.a(gmx_parallel_3dfft.o) _gmx_parallel_transpose_xy in libmd_mpi.a(gmx_parallel_3dfft.o) _lam_mpi_int, referenced from: _make_dd_communicators in libmd_mpi.a(domdec.o) _make_dd_communicators in libmd_mpi.a(domdec.o) _make_dd_communicators in libmd_mpi.a(domdec.o) _gmx_sumi_sim
Re: [gmx-users] Re: Minimum simulation time needed to have a completely minimized structure
so how shall i proceed now ... can u guide ?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] segmentation fault with grompp
I just used this topology in conjunction with popc128a.pdb (with some naming adjustments to match the topologies), and everything worked fine. I am using version 4.0.5, as well. Are you running grompp on a local workstation, or on a remote filesystem? I have noticed sporadic, unpredictable seg faults in grompp which I presume are due to NFS blips on our cluster. Have you recompiled without --enable-mpi, as I suggested before? I don't know if that's the problem or not; do other systems (proteins in water, or something else reasonably simple) result in the same problem? -Justin Gard Nelson wrote: Ok, here's my topology file: ; Include forcefield parameters #include ffgmx.itp #include lipid.itp ; Include Lipid Topologies #include popc.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Berger Membrane in water [ molecules ] ; Compound#mols POP 128 SOL 2460 and here's my ff_dum.itp: ; These constraints are used for dummy constructions as generated by pdb2gmx. ; Values depend on the details of the forcefield, vis. bondlengths and angles ; These parameters are designed to be used with the GROMACS forcefields ; ffgmx and ffgmx2 and with the GROMOS96 forcefields G43a1, G43a2 and G43b1. ; Constraints for the rigid NH3/CH3 groups depend on the hygrogen mass, ; since an increased hydrogen mass translates into increased momentum of ; inertia which translates into a larger distance between the dummy masses. #ifdef HEAVY_H ; now the constraints for the rigid NH3 groups #define DC_MNC1 0.175695 #define DC_MNC2 0.188288 #define DC_MNMN 0.158884 ; now the constraints for the rigid CH3 groups #define DC_MCN 0.198911 #define DC_MCS 0.226838 #define DC_MCC 0.204247 #define DC_MCNR 0.199798 #define DC_MCMC 0.184320 #else ; now the constraints for the rigid NH3 groups #define DC_MNC1 0.144494 #define DC_MNC2 0.158002 #define DC_MNMN 0.079442 ; now the constraints for the rigid CH3 groups #define DC_MCN 0.161051 #define DC_MCS 0.190961 #define DC_MCC 0.166809 #define DC_MCNR 0.162009 #define DC_MCMC 0.092160 #endif ; and the angle-constraints for OH and SH groups in proteins: #define DC_CS 0.23721 #define DC_CO 0.19849 #define DC_PO 0.21603 Thanks for your help! Gard -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to calculate binding free energy and electrostatics potential for ligand-protein complex
hello How can we calculate binding free energy and electrostatics potential for ligand-protein complex? which parameter is required in mdrun input file for that? I tried online manual but did not get output. It is appriciable if any body have idea Thanks in advance Regards Pawan Gupta -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pairs interactions
Dears, One questions about pair interaction. I mean the one defined in the topology files under the [ pairs ]. They interaction with plain electrostatic, meaning without shift, switch function applied to it. If it was possible to change this, it would be pretty nice, unless there are specific use for this ... The question: Does the pairs electrostatic interactions include an eventual epsilon ? Thanks, XAvier. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.
Hello all, After minimizing the energy of my system of 200 particle coordinates of box dimension 3.5 nm to an acceptable value, I proceeded to doing mdrun but got the error message: Source code file: nsgrid.c, line: 348. Fatal error: Number of grid cells is zero. Probably the system and box collapsed. I was wondering what could be the cause. Below are my energy minimization parameter file, the results of the minimization and the mdrun parameter file. oxymin.mdp file title= NPT simulation of a Lennard-Jones Fluid cpp = /lib/cpp include = -I../top define = constraints = none integrator = steep nsteps = 5000 emtol= 1000 emstep = 0.10 nstlist = 10 rlist= 0.9 ns_type = grid coulombtype = PME rcoulomb = 0.9 vdwtype = cut-off rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 optimize_fft = yes Step= 673, Dmax= 6.9e-03 nm, Epot= 6.11020e+05 Fmax= 7.64685e+03, atom= 19 Step= 675, Dmax= 4.1e-03 nm, Epot= 6.10956e+05 Fmax= 1.71624e+03, atom= 53 Step= 677, Dmax= 2.5e-03 nm, Epot= 6.10933e+05 Fmax= 3.60118e+03, atom= 30 Step= 678, Dmax= 3.0e-03 nm, Epot= 6.10927e+05 Fmax= 3.03499e+03, atom= 19 Step= 679, Dmax= 3.6e-03 nm, Epot= 6.10915e+05 Fmax= 4.80541e+03, atom= 30 Step= 680, Dmax= 4.3e-03 nm, Epot= 6.10913e+05 Fmax= 4.79865e+03, atom= 19 Step= 681, Dmax= 5.2e-03 nm, Epot= 6.10910e+05 Fmax= 6.50875e+03, atom= 30 Step= 683, Dmax= 3.1e-03 nm, Epot= 6.10857e+05 Fmax= 9.58182e+02, atom= 160 writing lowest energy coordinates. Back Off! I just backed up oxymin.gro to ./#oxymin.gro.6# Steepest Descents converged to Fmax 1000 in 684 steps Potential Energy = 6.1085662e+05 Maximum force = 9.5818250e+02 on atom 160 Norm of force = 2.9207101e+02 oxymdrun.mdp file title= NPT simulation of a LJ FLUID cpp = /lib/cpp include = -I../top define = integrator = md ; a leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 ; time-step in ps nsteps = 50 ; total number of steps; total time (1 ns) nstcomm = 1 ; frequency for com removal nstxout = 1000 ; freq. x_out nstvout = 1000 ; freq. v_out nstfout = 0 ; freq. f_out nstlog = 500; energies to log file nstenergy= 500; energies to energy file nstlist = 10 ; frequency to update neighbour list ns_type = grid ; neighbour searching type rlist= 0.9; cut-off distance for the short range neighbour list coulombtype = PME; particle-mesh-ewald electrostatics rcoulomb = 0.9; distance for the coulomb cut-off vdw-type = Cut-off; van der Waals interactions rvdw = 0.9; distance for the LJ or Buckingham cut-off fourierspacing = 0.12 ; max. grid spacing for the FFT grid for PME fourier_nx = 0 ; highest magnitude in reciprocal space when using Ewald fourier_ny = 0 ; highest magnitude in reciprocal space when using Ewald fourier_nz = 0 ; highest magnitude in reciprocal space when using Ewald pme_order= 4 ; cubic interpolation order for PME ewald_rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential optimize_fft = yes; calculate optimal FFT plan for the grid at start up. DispCorr = no ; Tcoupl = nose-hoover; temp. coupling with vel. rescaling with a stochastic term. tau_t= 0.5; time constant for coupling tc-grps = OXY; groups to couple separately to temp. bath ref_t= 80 ; ref. temp. for coupling Pcoupl = parrinello-rahman ; exponential relaxation pressure coupling (box is scaled every timestep) Pcoupltype = isotropic ; box expands or contracts evenly in all directions (xyz) to maintain proper pressure tau_p= 0.9; time constant for coupling (ps) compressibility = 4.5e-5 ; compressibility of solvent used in simulation ref_p= 1.0; ref. pressure for coupling (bar) gen_vel = yes; generate velocities according to a Maxwell distr. at gen_temp gen_temp
Re: [gmx-users] pairs interactions
Well ... the answer is yes: pairs interactions are scaled by if epsilon different than 1.0 is defined in the mdp file ... but easier to fix that the shift/switch thingy ... Another point (more scary) is that using fudge LJ = 0.0 does not turn off the pairs LJ interactions; fudge QQ does for electrostatic! this is using the standard gmx-4.0.7 ... --- some numbers for the purists: epsilon = 2.5; fudge LJ = 1.0; fudge QQ = 0.5 Step Time Lambda 00.00.0 Energies (kJ/mol) BondTab. Angles Improper Dih. Tab. Dih. LJ-14 1.56855e+023.84067e+011.68183e+01 -1.36500e+03 2.26253e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Kinetic En. 7.92958e+01 -1.41790e+05 -2.97492e+02 -1.43139e+05 2.07062e+04 Total EnergyTemperature Pressure (bar) -1.22432e+053.07112e+02 -2.18939e+01 epsilon = 25; fudge LJ = 1.0; fudge QQ = 0.5 Energies (kJ/mol) BondTab. Angles Improper Dih. Tab. Dih. LJ-14 1.56855e+023.84067e+011.68183e+01 -1.36500e+03 2.26253e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Kinetic En. 7.92958e+00 -1.41790e+05 -2.97493e+01 -1.42942e+05 2.07033e+04 Total EnergyTemperature Pressure (bar) -1.22239e+053.07069e+02 -2.01929e+01 epsilon = 25; fudge LJ = 0.0; fudge QQ = 0.5 Energies (kJ/mol) BondTab. Angles Improper Dih. Tab. Dih. LJ-14 1.56855e+023.84067e+011.68183e+01 -1.36500e+03 2.26253e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Kinetic En. 7.92958e+00 -1.41790e+05 -2.97493e+01 -1.42942e+05 2.07033e+04 Total EnergyTemperature Pressure (bar) -1.22239e+053.07069e+02 -2.01929e+01 epsilon = 25; fudge LJ = 0.0; fudge QQ = 0.0 Energies (kJ/mol) BondTab. Angles Improper Dih. Tab. Dih. LJ-14 1.56855e+023.84067e+011.68183e+01 -1.36500e+03 2.26253e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Kinetic En. 0.0e+00 -1.41790e+05 -2.97493e+01 -1.42950e+05 2.07033e+04 Total EnergyTemperature Pressure (bar) -1.22247e+053.07069e+02 -2.02610e+01 On Feb 10, 2010, at 5:59 PM, XAvier Periole wrote: Dears, One questions about pair interaction. I mean the one defined in the topology files under the [ pairs ]. They interaction with plain electrostatic, meaning without shift, switch function applied to it. If it was possible to change this, it would be pretty nice, unless there are specific use for this ... The question: Does the pairs electrostatic interactions include an eventual epsilon ? Thanks, XAvier. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Load balancing between PME and PP on more than 12 processors
Hi, Have a look at g_tunepme on the gromacs web site or on google. It does this fine tuning for you. It is pretty good On Feb 10, 2010, at 21:09, Warren Gallin wgal...@ualberta.ca wrote: I have a question about the procedure for running a parallel simulation on more than 12 processors using GROMACS 4.0.7. I understand that partitioning the PME calculations and PP calculations improves performance, and that there is an initial automated guess at deciding how many processors to devote to PME vs. PP calculations. When I ran a simulation of a system on 16 processors, GROMACS automatically devoted 6 processors to PMA calculations and 10 to PP calculations. A 1 nsec simulation using 2 fs steps took only marginally less time (5 h 12 m) as runningthe same simulation on 8 processors (6 h 45 m), without the separation of PME and PP calculations and the following note was in the log file: NOTE: 35.7 % performance was lost because the PME nodes had more work to do than the PP nodes. You might want to increase the number of PME nodes or increase the cut-off and the grid spacing. I reran the same simulation, this time including -npme 8 in the mdrun call, and the simulation completed in 4 h 19 min, with the following note in the log file: NOTE: 16.8 % performance was lost because the PME nodes had more work to do than the PP nodes. You might want to increase the number of PME nodes or increase the cut-off and the grid spacing. So I conclude that I need to increase cut-off and grid spacing, since this is recommended in the manual and in the paper describing the GROMACS 4 algoithm changes. Unfortunately a) I am unclear on which parameters in the .mdp file represent cut- off and grid spacing and b) When the manual says For changing the electrostatics settings it is useful to know the accuracy of the electrostatics remains nearly constant when the Coulomb cut-off and the PME grid spacing are scaled by the same factor. Does this mean that cut-off and grid-spacing parameters need to be changed by the same proportion? I hope this is sufficiently specific a question - if not, let me knwo what I need to be clearer on. Thanks, Warren Gallin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_cluster group for output
Hi all, I would really appreciate if someone can help me with the group for output option on g_cluster. When I use g_cluster, it asks me to select two groups. A gourd for fit and RMSD calculation and a group for output: Select group for least squares fit and RMSD calculation: Group 0 ( System) has 205722 elements Group 1 ( Protein) has 10337 elements Group 2 ( Protein-H) has 8036 elements Group 3 ( C-alpha) has 1005 elements Select group for output: Group 0 ( System) has 205722 elements Group 1 ( Protein) has 10337 elements Group 2 ( Protein-H) has 8036 elements Group 3 ( C-alpha) has 1005 elements Know, I have always assumed that g_cluster do a fit and calculate the RMSD matrix based on the trajectory of the first group, and the second group is just for control what atoms will be written to the output file. Recently, however, I did some tests and it seems that the different groups chosen for output group effect not only the atoms written to the output file, but also the clustering results. Can anyone confirm this? Cheers, Itamar -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@med.monash.edu.au the second 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] concaternating remd trajectories using trjcat demux
Dear gromacs users, I am trying to collect trajectories corresponding to each temperature by using trjcat with demux. There were similar issues posted earlier, but I do not see the solution on the problem I am facing following: I have 64 replicas simulated using namd in dcd trajectory format and saved them in gromacs format (.trr) using vmd. I inspected the gromacs format trajectories by eyes in vmd and looked fine. However, when I tried trjcat -f g*.trr -demux replica_index.xvg, the output looked weird. So I tested a small set of the trajectories (using only replicas 0 to 8 and first two frames) and noticed that the output does not match to the replica_index.xvg file. trjcat -f *g*.trr -demux replica_index.xvg replica_index.xvg 0 0 1 2 3 4 5 7 6 2 1 0 2 3 5 4 6 7 I am using Ubuntu (32bit) and the gromas version is 4.0.5. 0_trajout.xtc should have the 1st frame from replica 0 and 2nd frame from replica 1, but both frames for 0_trajout.xtc are from the replica 0. It seems the index file does not cooperate properly with the trjcat and -demux. Does anyone have clue about this? Many thanks, Segun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] concaternating remd trajectories using trjcat demux
Segun Jung wrote: Dear gromacs users, I am trying to collect trajectories corresponding to each temperature by using trjcat with demux. There were similar issues posted earlier, but I do not see the solution on the problem I am facing following: Like what? It will save time if you can post links to these similar issues to avoid posting non-solutions that have already been ruled out. I have 64 replicas simulated using namd in dcd trajectory format and saved them in gromacs format (.trr) using vmd. I inspected the gromacs format trajectories by eyes in vmd and looked fine. However, when I tried trjcat -f g*.trr -demux replica_index.xvg, the output looked weird. So I tested a small set of the trajectories (using only replicas 0 to 8 and first two frames) and noticed that the output does not match to the replica_index.xvg file. If you ran your simulations with NAMD, how did you generate this file? In Gromacs, one would run demux.pl on the md.log file. I presume NAMD prints different output. trjcat -f *g*.trr -demux replica_index.xvg replica_index.xvg 0 0 1 2 3 4 5 7 6 2 1 0 2 3 5 4 6 7 If you analyzed replicas 0 to 8 (inclusive) then you should have an 8 somewhere, right? I am using Ubuntu (32bit) and the gromas version is 4.0.5. 0_trajout.xtc should have the 1st frame from replica 0 and 2nd frame from replica 1, but both frames for 0_trajout.xtc are from the replica 0. This might go along with my comment above. If there are nine replicas (0 to 8), then there may be some mis-translation of the .xvg file. It seems the index file does not cooperate properly with the trjcat and -demux. Does anyone have clue about this? I know I can attest to demultiplexing working as advertised, so I assume intact trajectories with a correct index file should work properly. You have a few variables to deal with: .dcd-.trr translation, however you generated the .xvg file, and if you've even told us the right number of replicas, among perhaps others. Also, what does gmxcheck tell you about each of the .trr files? Do they contain what you would expect them to? -Justin Many thanks, Segun -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulations in parallel using the pull code
Dear Gromacs community, I modified the pull code in GROMACS to apply forces on atoms that are in a certain region of space. It compiles error free and runs fine to give me the expected results. I then recompiled with mpi support. The cluster I am using has 8 cores/processors per node. When I use 1, 2 or 4 nodes to run, I get identical results, but the results are very different when I run parallel on all 8 cores. 1. I am not sure how the forces I apply in the pull code are parallelized. 2. Is this easy for me to edit in the source code or is it best if I use only upto 4 processors for my job? 3. Will the number of processors that I am able to use change depending on the system size? I currently have on protein and about 7500 water molecules to give a total of about 25000 atoms. I am using SHAKE with constraints on h-bonds. Thanks for any help! Sumanth Sumanth N Jamadagni Graduate Student Isermann Dept of Chemical and Biological Engg Rensselaer Polytechnic Institute jam...@rpi.edu (Cell)518-598-2786 http://boyle.che.rpi.edu/~sumanth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] follow up: simulations in parallel using the pull code
As a follow up to my post (pasted below), I am providing some more details. 1. I am applying forces on heavy atoms (water oxygens and protein non-hydrogens). 2. I tried switching of SHAKE. Results improve marginally, but the 8 processor data are still wrong. 3. There is no pressure coupling. I have left a vapor layer of a few nanometers to allow for any density changes. I hope this further information helps in debugging. Thanks Sumanth Jamadagni Dear Gromacs community, I modified the pull code in GROMACS to apply forces on atoms that are in a certain region of space. It compiles error free and runs fine to give me the expected results. I then recompiled with mpi support. The cluster I am using has 8 cores/processors per node. When I use 1, 2 or 4 nodes to run, I get identical results, but the results are very different when I run parallel on all 8 cores. 1. I am not sure how the forces I apply in the pull code are parallelized. 2. Is this easy for me to edit in the source code or is it best if I use only upto 4 processors for my job? 3. Will the number of processors that I am able to use change depending on the system size? I currently have on protein and about 7500 water molecules to give a total of about 25000 atoms. I am using SHAKE with constraints on h-bonds. Thanks for any help! Sumanth Sumanth N Jamadagni Graduate Student Isermann Dept of Chemical and Biological Engg Rensselaer Polytechnic Institute jam...@rpi.edu (Cell)518-598-2786 http://boyle.che.rpi.edu/~sumanth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] A question about dihedral angles
On 11/02/10 06:52, Amir Marcovitz wrote: Hi all, i think my question is kind of trivial but i'll ask it any way: suppose you have atoms that are arranged on the XY plane in a square lattice arrangment with a spacing of 1. you bond them , add angles etc. and now you want to add proper dihedral angles using function 1. What i know, is that the dihedral angle 'phi' between a quartet of atoms i,j,k,l is the angle between the two surface i,j,k and j,k,l. (i think this is also written in the manual..) yet, i experience some problems with a system similar to the one i described above - i.e., the planar geometry of the atoms gets twisted until it blows up which make me confused and think that i may did some mistakes in defining these angles in the [ dihedrals ] section of the topology file. I think this is all covered in chapter 4 of the manual. Mark it could realy be useful if someone can tell me the value of the dihedral phi for the following quartets (given the x,y coordinates): 1) i (0,0) , j (0,1) , k (1,1) , l(1,2) 2) i(0,0) , j (1,0) , k(2,0) , l(3,0) 3)i(0,0) , j(1,0) , k (2,0),l(2,1) 4 ) i(0,0) , j(1,0) , k(1,1) , l(0,1) i think that 1 is 180 degrees , and 2,3,4 are 0 degrees am i right? is there a difference between 0 and 180? (i used a multipilicty of 2) i.e., it looks like [ dihedrals ] ; ai aj ak al funct phi cp mult 7 1 2 31 0.00e+00 3.347200e+01 2.00e+00 14 8 9 151 1.80e+02 3.347200e+01 2.00e+00 and so on.. sorry for the bizzare question.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs 4.0.7 compilation problem
On 11/02/10 01:55, sarbani chattopadhyay wrote: Hi , I want to install gromacs 4.0.7 in double precision in a 64 bit Mac computer with 8 nodes. I got the lam7.1.4 source code files and installed them using the following commands ./configure --without-fc ( it was giving an error for the fortran compiler) make make install then I get the gromacs 4.0.7 source code files and installed it as ./configure --disable-float make make install After that I try get the mpi version for mdrun make clean ./configure --enable-mpi --disable-nice --program-suffix=_mpi make mdrun I GET ERROR IN THIS STEP , With error message undefined symbols: _lam_mpi_double, referenced from: Apparently the linker can find some MPI libraries during configure, but can't find the right ones during compilations. I suggest checking for and removing other MPI libraries, or using OpenMPI rather than the deprecated LAM, and reading their documentation for how to install correctly on your OS. Any way, this is not a problem specific to GROMACS. Mark _gmx_sumd_sim in libgmx_mpi.a(network.o) _gmx_sumd in libgmx_mpi.a(network.o) _gmx_sumd in libgmx_mpi.a(network.o) _wallcycle_sum in libmd_mpi.a(gmx_wallcycle.o) _lam_mpi_byte, referenced from: _exchange_rvecs in repl_ex.o _replica_exchange in repl_ex.o _replica_exchange in repl_ex.o _replica_exchange in repl_ex.o _finish_run in libmd_mpi.a(sim_util.o) _dd_collect_vec in libmd_mpi.a(domdec.o) _dd_collect_vec in libmd_mpi.a(domdec.o) _set_dd_cell_sizes in libmd_mpi.a(domdec.o) _dd_distribute_vec in libmd_mpi.a(domdec.o) _dd_distribute_vec in libmd_mpi.a(domdec.o) _dd_partition_system in libmd_mpi.a(domdec.o) _partdec_init_local_state in libmd_mpi.a(partdec.o) _partdec_init_local_state in libmd_mpi.a(partdec.o) _gmx_rx in libmd_mpi.a(partdec.o) _gmx_tx in libmd_mpi.a(partdec.o) _gmx_bcast_sim in libgmx_mpi.a(network.o) _gmx_bcast in libgmx_mpi.a(network.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _gmx_pme_do in libmd_mpi.a(pme.o) _write_traj in libmd_mpi.a(stat.o) _write_traj in libmd_mpi.a(stat.o) _gmx_pme_receive_f in libmd_mpi.a(pme_pp.o) _gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_send_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_send_force_vir_ener in libmd_mpi.a(pme_pp.o) _gmx_pme_send_force_vir_ener in libmd_mpi.a(pme_pp.o) _gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o) _gmx_pme_recv_q_x in libmd_mpi.a(pme_pp.o) _dd_gatherv in libmd_mpi.a(domdec_network.o) _dd_scatterv in libmd_mpi.a(domdec_network.o) _dd_gather in libmd_mpi.a(domdec_network.o) _dd_scatter in libmd_mpi.a(domdec_network.o) _dd_bcastc in libmd_mpi.a(domdec_network.o) _dd_bcast in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv2_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv_rvec in libmd_mpi.a(domdec_network.o) _dd_sendrecv_int in libmd_mpi.a(domdec_network.o) _dd_sendrecv_int in libmd_mpi.a(domdec_network.o) _dd_sendrecv_int in libmd_mpi.a(domdec_network.o) _lam_mpi_prod, referenced from: _gprod in do_gct.o _do_coupling in do_gct.o _do_coupling in do_gct.o _do_coupling in do_gct.o _lam_mpi_float, referenced from: _gprod in do_gct.o _do_coupling in do_gct.o _do_coupling in do_gct.o _do_coupling in do_gct.o _gmx_tx_rx_real in libmd_mpi.a(partdec.o) _gmx_sumf_sim in libgmx_mpi.a(network.o) _gmx_sumf in libgmx_mpi.a(network.o) _gmx_sumf in libgmx_mpi.a(network.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _gmx_sum_qgrid_dd in libmd_mpi.a(pme.o) _pmeredist in libmd_mpi.a(pme.o) _gmx_pme_init in libmd_mpi.a(pme.o) _gmx_sum_qgrid in libmd_mpi.a(pme.o) _gmx_sum_qgrid in libmd_mpi.a(pme.o) _gmx_parallel_transpose_xy in libmd_mpi.a(gmx_parallel_3dfft.o) _gmx_parallel_transpose_xy in libmd_mpi.a(gmx_parallel_3dfft.o) _lam_mpi_int, referenced from: _make_dd_communicators in libmd_mpi.a(domdec.o) _make_dd_communicators in libmd_mpi.a(domdec.o) _make_dd_communicators in libmd_mpi.a(domdec.o) _gmx_sumi_sim in libgmx_mpi.a(network.o) _gmx_sumi in libgmx_mpi.a(network.o) _gmx_sumi in libgmx_mpi.a(network.o) _pmeredist in libmd_mpi.a(pme.o) _lam_mpi_sum, referenced from:
[gmx-users] Software inconsistency error: Not enough water
Hello gmxusers !! I am simulating a protein and it is bound to ATP. Simulation of protein alone (without) works fine. Solely ATP simulation too works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb) file. Error: $ genion -s em.tpr -o ion.pdb -p topol.top -np 48 WARNING: turning of free energy, will use lambda=0 Reading file em.tpr, VERSION 4.0.7 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 48 Na ions and 0 Cl ions. Select a continuous group of solvent molecules Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 70056 elements Group 1 ( Protein) has 10214 elements Group 2 ( Protein-H) has 5107 elements Group 3 ( C-alpha) has 623 elements Group 4 (Backbone) has 1869 elements Group 5 ( MainChain) has 2488 elements Group 6 (MainChain+Cb) has 3083 elements Group 7 ( MainChain+H) has 3099 elements Group 8 ( SideChain) has 7115 elements Group 9 ( SideChain-H) has 2619 elements Group10 ( Prot-Masses) has 10214 elements Group11 ( Non-Protein) has 59842 elements Group12 ( ATP) has43 elements Group13 ( SOL) has 59799 elements Group14 ( Other) has 59842 elements Select a group: 13 Selected 13: 'SOL' Number of (3-atomic) solvent molecules: 19933 Processing topology Back Off! I just backed up temp.top to ./#temp.top.1# --- Program genion, VERSION 4.0.7 Source code file: gmx_genion.c, line: 269 Software inconsistency error: Not enough water --- Though my system has sufficient amount of water (19933) molecules. Can not understand the error. Any information would be useful. Chadan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
