[gmx-users] Re: gmx-users Digest, Vol 79, Issue 167
Hi Tom. Hi, You show differences when using GROMACS 4.5.3 for one simulation with the pdb2gmx option -nochargegrp and one without this option (is this correct, or did you manually edit the topology to have the old charge groups?). This pdb2gmx option should have no effect in 4.5.3 as all the entries in the CHARMM27 .rtp are in individual charge groups. I will try to be more clear here: First step: The two top files were generated with different rtp files. In the first case i used a rtp file where the charge groups for each AA were distributed as in the CHARMM27 ff distribution. The top file were generated the gromacs (4.0.5) and the following command pdb2gmx_mpi -ignh -ff charmm27 -ter -f hMRP1_K-TM17_AcAm.pdb -o hMRP1_K-TM17.gro -p hMRP1_K-TM17.top -missing For the second top i used gromacs 4.5 with the argument -nochargegrp (with one charge group assigned for atom) with the command pdb2gmx_mpi -ignh -ff charmm27 -ter -f hMRP1_K-TM17_AcAm-H.pdb -o hMRP1_K-TM17.gro -p hMRP1_K-TM17.top -missing -nochargegrp Second Step: i used the latest version of gromacs 4.5.3 to generate the different tpr files and performed the simulations with the two types of top files. In case of the MD with the others versions of gromacs, the step two was done with the cooresponding version of gromacs. If you didn't edit the 4.5.3 topology then either you are doing something else different between these simulations or what you think is a difference between simulations with and without this pdb2gmx option is just a coincidence and that your peptide is sometimes stable over this short 24 ns simulation and sometimes it unfolds, irrespective of the charge group option. I have also performed a MD during 100 ns (with -chargegroup), and in this case the peptide remains stable along the simulation time. I don't understand why. Moreover i dont think it is a coincidence since i observe the same results whatever the gmx version and md parameters used If you did edit the topology then are you sure that it is correct? Did you use 4.5.3 to get the topology and edit it by hand or did you generate this 'charge group' topology by some other method, such as another version of GROMACS? If you used the topology from 4.0.x then maybe there are issues here as I know CHARMM27 was not fully supported until 4.5. I didn't edit the top file manually, i used only the pdb2gmx tool. However by reading your message, i have take a look more deeper in te the top file and i have found differences in some directives (for example in the pair directive where there are more terms). =-O To be sure that this difference has no impact in the MD, i going to do other MD. I will come back soon. Thanks you again SA Cheers Tom On 25/11/10 22:42, sa wrote: Dear All, In a previous message (http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html ), I described the results obtained with MD performed with the CHARMM27 ff and the chargegrp yes and no options of a peptide in TIP3P water simulated gromacs. Since these results puzzled me a lot, i would like to share with you others results obtained from the gromacs community advices to explain these results. In few words, the context of these simulations. One of my labmate did, 8 months ago (march/april), several simulations of a peptide (25 AA) with the CHARMM27 ff (and CMAP). The peptide is a transmembrane segment (TM) and belongs to a large membrane protein. This TM segment has an initial helical conformation. The simulations were performed in a cubic box filled with app. 14000 TIP3P water (Jorgensen's model) with 2 Cl ions. To construct the topology file of the system, -chargegrp yes with pdb2gmx and the MD were done with the gromacs 4.0.5. For some reasons, he had to left the lab, and my boss asked me to continue his work. When I checked their results, i was very intrigued by these MD results because he found that the peptide keep along all the simulation time (100 ns) its initial helical conformation. This results are not in agreement with circular dichroism experiments which are shown that the same peptide in water has no helix segment and is completely unfold. I am aware that the simulation time is short compared to experiment time scale, however since i haven't seen any unfolding events in this simulation, so I was not very confident about these results. To explain this inconsistency, I have suspected that the error came probably of the use of the default -chargegrp with CHARMM ff in these simulations since i have read several recent threads about the charge groups problems in the CHARMM ff implementation in gromacs. To examine this hypothesis I have done two simulations with last gromacs version (4.5.3) and two top files containing charge groups and no charge groups for the peptide residus. I used the *same* initial pdb file, box size and simulations parameters. The two simulations
Re: [gmx-users] Re: gmx-users Digest, Vol 79, Issue 167
OK that makes things clearer. As I mentioned I would check that it is not an issue with using CHARMM from 4.0.5 as if I remember correctly the CHARMM forcefield was not fully supported until version 4.5 (and I think was removed from the GROMACS 4.0.7 release so people didn't use it). As I also mentioned someone else will know much more about this than me, for example what changed between the 4.0.5 version of the forcefield implementation and the 4.5 implementation. It may have been very little, but I do not know. As for you seeing the same with different GROMACS versions then I think this does not matter as you are using the same 4.0.5 topology with the different versions and it could be this topology which is causing the issues. The test to run to check if it is the charge groups which are causing this behavior is to run simulations (probably with repeats so you sure) using GROMACS 4.5.1 with and without the -nochargegrp option of pdb2gmx and everything else the same. As to why you are seeing this (if it is indeed something you can confirm) is another question and I am unsure, it seems fairly strange. Again I am sure someone else with more knowledge can comment on this. Cheers Tom On 26/11/10 08:35, sa wrote: Hi Tom. Hi, You show differences when using GROMACS 4.5.3 for one simulation with the pdb2gmx option -nochargegrp and one without this option (is this correct, or did you manually edit the topology to have the old charge groups?). This pdb2gmx option should have no effect in 4.5.3 as all the entries in the CHARMM27 .rtp are in individual charge groups. I will try to be more clear here: First step: The two top files were generated with different rtp files. In the first case i used a rtp file where the charge groups for each AA were distributed as in the CHARMM27 ff distribution. The top file were generated the gromacs (4.0.5) and the following command pdb2gmx_mpi -ignh -ff charmm27 -ter -f hMRP1_K-TM17_AcAm.pdb -o hMRP1_K-TM17.gro -p hMRP1_K-TM17.top -missing For the second top i used gromacs 4.5 with the argument -nochargegrp (with one charge group assigned for atom) with the command pdb2gmx_mpi -ignh -ff charmm27 -ter -f hMRP1_K-TM17_AcAm-H.pdb -o hMRP1_K-TM17.gro -p hMRP1_K-TM17.top -missing -nochargegrp Second Step: i used the latest version of gromacs 4.5.3 to generate the different tpr files and performed the simulations with the two types of top files. In case of the MD with the others versions of gromacs, the step two was done with the cooresponding version of gromacs. If you didn't edit the 4.5.3 topology then either you are doing something else different between these simulations or what you think is a difference between simulations with and without this pdb2gmx option is just a coincidence and that your peptide is sometimes stable over this short 24 ns simulation and sometimes it unfolds, irrespective of the charge group option. I have also performed a MD during 100 ns (with -chargegroup), and in this case the peptide remains stable along the simulation time. I don't understand why. Moreover i dont think it is a coincidence since i observe the same results whatever the gmx version and md parameters used If you did edit the topology then are you sure that it is correct? Did you use 4.5.3 to get the topology and edit it by hand or did you generate this 'charge group' topology by some other method, such as another version of GROMACS? If you used the topology from 4.0.x then maybe there are issues here as I know CHARMM27 was not fully supported until 4.5. I didn't edit the top file manually, i used only the pdb2gmx tool. However by reading your message, i have take a look more deeper in te the top file and i have found differences in some directives (for example in the pair directive where there are more terms). =-O To be sure that this difference has no impact in the MD, i going to do other MD. I will come back soon. Thanks you again SA Cheers Tom On 25/11/10 22:42, sa wrote: Dear All, In a previous message (http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html), I described the results obtained with MD performed with the CHARMM27 ff and the chargegrp yes and no options of a peptide in TIP3P water simulated gromacs. Since these results puzzled me a lot, i would like to share with you others results obtained from the gromacs community advices to explain these results. In few words, the context of these simulations. One of my labmate did, 8 months ago (march/april), several simulations of a peptide (25 AA) with the CHARMM27 ff (and CMAP). The peptide is a transmembrane segment (TM) and belongs to a large membrane protein. This TM segment has an initial helical conformation. The simulations were performed in
Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)
Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories! Can anyone find the reason causing such error? regards, Baofu Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: Hi, as a workaround you could run with -noappend and later concatenate the output files. Then you should have no problems with locking. Carsten On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of Function not implemented? Any suggestion is appreciated! * Getting Loaded... Reading file pre.tpr, VERSION 4.5.3 (single precision) Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010 --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 1750 Fatal error: Failed to lock: pre.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Doesn't Have to Be Tip Top (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 64 gcq#147: It Doesn't Have to Be Tip Top (Pulp Fiction) -- 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. -- -- mpiexec has exited due to process rank 0 with PID 32758 on -- 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 -- Dr. Baofu Qiao Institute for Computational Physics Universität Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49(0)711 68563607 Fax: +49(0)711 68563658 -- 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] Free Energy Calculation: dVpot/dlambda is always zero
Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?
To see if the problem is force-field related, you could try to run the same simulations using amber-ff. If you will find the same results, probably is a software bug. Maybe the bug has been introduced in the version 4 when the Domain Decomposition has been introduced. You can check if it is a software problem using the 3.3.3 version. Il 25/11/2010 23:42, sa ha scritto: Dear All, In a previous message (http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html), I described the results obtained with MD performed with the CHARMM27 ff and the chargegrp yes and no options of a peptide in TIP3P water simulated gromacs. Since these results puzzled me a lot, i would like to share with you others results obtained from the gromacs community advices to explain these results. In few words, the context of these simulations. One of my labmate did, 8 months ago (march/april), several simulations of a peptide (25 AA) with the CHARMM27 ff (and CMAP). The peptide is a transmembrane segment (TM) and belongs to a large membrane protein. This TM segment has an initial helical conformation. The simulations were performed in a cubic box filled with app. 14000 TIP3P water (Jorgensen's model) with 2 Cl ions. To construct the topology file of the system, -chargegrp yes with pdb2gmx and the MD were done with the gromacs 4.0.5. For some reasons, he had to left the lab, and my boss asked me to continue his work. When I checked their results, i was very intrigued by these MD results because he found that the peptide keep along all the simulation time (100 ns) its initial helical conformation. This results are not in agreement with circular dichroism experiments which are shown that the same peptide in water has no helix segment and is completely unfold. I am aware that the simulation time is short compared to experiment time scale, however since i haven't seen any unfolding events in this simulation, so I was not very confident about these results. To explain this inconsistency, I have suspected that the error came probably of the use of the default -chargegrp with CHARMM ff in these simulations since i have read several recent threads about the charge groups problems in the CHARMM ff implementation in gromacs. To examine this hypothesis I have done two simulations with last gromacs version (4.5.3) and two top files containing charge groups and no charge groups for the peptide residus. I used the *same* initial pdb file, box size and simulations parameters. The two simulations were carried out during 24 ns in the NPT ensemble with the md.mdp parameters described below after energy minimisation, NVT and NPT equilibration steps. constraints = all-bonds integrator = md nsteps = 1200 ; 24000ps ou 24ns dt = 0.002 nstlist = 10 nstcalcenergy = 10 nstcomm = 10 continuation= no; Restarting after NPT vdw-type= cut-off rvdw= 1.0 rlist = 0.9 coulombtype = PME rcoulomb = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 optimize_fft= yes nstvout = 5 nstxout = 5 nstenergy = 2 nstlog = 5000 ; update log file every 10 ps nstxtcout = 1000 ; frequency to write coordinates to xtc trajectory every 2 ps Tcoupl = nose-hoover tc-grps = Protein Non-Protein tau-t = 0.4 0.4 ref-t = 298 298 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 3.0 compressibility = 4.5e-5 ref_p = 1.0135 gen_vel = no I found that with charge groups, the peptide remains in its initial helical conformation, whereas with no charge group, the peptide unfolds quickly and has a random coil conformation. I have shown these results to my boss but I was not able to explain why we observe these differences between the two simulations. Indeed since i use PME in the MD, chargegroup should not affect the dynamic results (correct ?) . He asked to do others simulations with different versions of gromacs to see if is not a bug with charge group implementation in gromacs. For testing i have done four others MD wit the *same* initial pdb file, box size and simulations parameters and with previous GMX version 4.5.0 and pre 4.5.2 and with the two types of top files. In addition since i have done simulations with non optimal parameter for the vdW et electrostatic, i have also tested the influence of the vdW et electrostatic MD parameters on the MD by performing two additional simulations with the parameters used in the Bjelkmar et al . paper (J. Chem. Theory Comput. 2010, 6, 459–466) (labeled GMX4.5.3 CHARMM in the figures) ; Run parameters integrator
[gmx-users] Phosphorylated Serine in charmm
Hello all, I am using charmm ff in Gromacs 4.5.2, everything goes right with standard proteins, but now i want to run a simulation on a protein with a phosphorylated residue. As mentionned in this post http://www.mail-archive.com/gmx-users@gromacs.org/msg35532.html, I changed the rtp and hbd to add a specific section for the phosphorylated amino-acid, having checked the parametres with charmm. I still have the problem in pdb2gmx where it seems like he can't see the new definition and gives me the residue topology database error. Is there another file where I have to specify the new amino-acids, I search all the files in the charmm directory in gromacs top, but I still can't find another place where amino-acids are defined. Thanks for you help -- 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] system is exploding
Dear gromacs users, I am trying to run simulations for small molecules in water. Topology files I created by my self for charm ff. When I am trying to start energy minimization I got an error: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = 1000 That's means my system is exploding. Please can you advice me on this, what I need to check. best, Olga -- 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] system is exploding
Have you run the energy minimization (or further simulation to optimize the structure and test the FF) on the small molecule before you added it into water? On 11/26/2010 11:26 AM, Olga Ivchenko wrote: Dear gromacs users, I am trying to run simulations for small molecules in water. Topology files I created by my self for charm ff. When I am trying to start energy minimization I got an error: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = 1000 That's means my system is exploding. Please can you advice me on this, what I need to check. best, Olga -- Dr. Baofu Qiao Institute for Computational Physics Universität Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49(0)711 68563607 Fax: +49(0)711 68563658 -- 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] system is exploding
I tried today to run minimization in vacuum for my small molecules. This has the same error. 2010/11/26 Baofu Qiao qia...@gmail.com Have you run the energy minimization (or further simulation to optimize the structure and test the FF) on the small molecule before you added it into water? On 11/26/2010 11:26 AM, Olga Ivchenko wrote: Dear gromacs users, I am trying to run simulations for small molecules in water. Topology files I created by my self for charm ff. When I am trying to start energy minimization I got an error: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = 1000 That's means my system is exploding. Please can you advice me on this, what I need to check. best, Olga -- Dr. Baofu Qiao Institute for Computational Physics Universität Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49(0)711 68563607 Fax: +49(0)711 68563658 -- 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] heme
Hi Erik I am using ffG43a1 force field. It has heme topology. But in Cyt C. FE is bonded to both NR of HIS and SD of MET. The parameter for the bond, FE SD, angles e.g. NR (HIS) FE SD(MET) and dihedral angle CH2(MET) SD (MET) FE NR(HIS) is missing in this force field. hence I am getting error while running grompp. Please suggest me what should I do. Shahid Nayeem On Thu, Nov 25, 2010 at 3:12 AM, Erik Marklund er...@xray.bmc.uu.se wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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] Re: Failed to lock: pre.log (Gromacs 4.5.3) Neither of 4.5.1, 4.5.2 and 4.5.3 works
Hi all, I just made some tests by using gmx 4.5.1, 4.5.2 and 4.5.3. Neither of them works on the continuation. --- Program mdrun, VERSION 4.5.1 Source code file: checkpoint.c, line: 1727 Fatal error: Failed to lock: pre.log. Already running simulation? --- Program mdrun, VERSION 4.5.2 Source code file: checkpoint.c, line: 1748 Fatal error: Failed to lock: pre.log. Already running simulation? --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 1750 Fatal error: Failed to lock: pre.log. Function not implemented. = The system to test is 895 SPC/E water,box size of 3nm, (genbox -box 3 -cs). The pre.mdp is attached. I have tested two clusters: Cluster A: 1)compiler/gnu/4.3 2) mpi/openmpi/1.2.8-gnu-4.3 3)FFTW 3.3.2 4) GMX 4.5.1/4.5.2/4.5.3 Cluster B: 1)compiler/gnu/4.3 2) mpi/openmpi/1.4.2-gnu-4.3 3)FFTW 3.3.2 4) GMX 4.5.3 GMX command: mpiexec -np 8 mdrun -deffnm pre -npme 2 -maxh 0.15 -cpt 5 -cpi pre.cpt -append Can anyone provide further help? Thanks a lot! best regards, On 11/26/2010 09:07 AM, Carsten Kutzner wrote: Hi, as a workaround you could run with -noappend and later concatenate the output files. Then you should have no problems with locking. Carsten On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of Function not implemented? Any suggestion is appreciated! * Getting Loaded... Reading file pre.tpr, VERSION 4.5.3 (single precision) Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010 --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 1750 Fatal error: Failed to lock: pre.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Doesn't Have to Be Tip Top (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 64 gcq#147: It Doesn't Have to Be Tip Top (Pulp Fiction) -- 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. -- -- mpiexec has exited due to process rank 0 with PID 32758 on pre.mdp Description: application/mdp -- 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] Free Energy Calculation: dVpot/dlambda is always zero
Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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] system is exploding
check your custom topology (this is where the error is 99% of the time), use qm minimized starting structures, make sure your structure matches your topology (atom names,numbers,ordering, etc.), test single molecules in vacuum first and/or reduce the step size of your SD minimizer. On 11/26/2010 11:47 AM, Baofu Qiao wrote: If you are really sure about the topology, the problem is the initial structure. Try to use PackMol to build it. On 11/26/2010 11:42 AM, Olga Ivchenko wrote: I tried today to run minimization in vacuum for my small molecules. This has the same error. 2010/11/26 Baofu Qiaoqia...@gmail.com Have you run the energy minimization (or further simulation to optimize the structure and test the FF) on the small molecule before you added it into water? On 11/26/2010 11:26 AM, Olga Ivchenko wrote: Dear gromacs users, I am trying to run simulations for small molecules in water. Topology files I created by my self for charm ff. When I am trying to start energy minimization I got an error: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = 1000 That's means my system is exploding. Please can you advice me on this, what I need to check. best, Olga -- Dr. Baofu Qiao Institute for Computational Physics Universität Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49(0)711 68563607 Fax: +49(0)711 68563658 -- 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] system is exploding
Quoting Baofu Qiao qia...@gmail.com: If you are really sure about the topology, the problem is the initial structure. Try to use PackMol to build it. For simple molecules in water, there is no need for a complicated program like packmol. Such a configuration can easily be built in Gromacs. I have yet to see any evidence of an error. From the original post, it seems that EM failed to start at all. -Justin On 11/26/2010 11:42 AM, Olga Ivchenko wrote: I tried today to run minimization in vacuum for my small molecules. This has the same error. 2010/11/26 Baofu Qiao qia...@gmail.com Have you run the energy minimization (or further simulation to optimize the structure and test the FF) on the small molecule before you added it into water? On 11/26/2010 11:26 AM, Olga Ivchenko wrote: Dear gromacs users, I am trying to run simulations for small molecules in water. Topology files I created by my self for charm ff. When I am trying to start energy minimization I got an error: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = 1000 That's means my system is exploding. Please can you advice me on this, what I need to check. best, Olga -- Dr. Baofu Qiao Institute for Computational Physics Universit�t Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49(0)711 68563607 Fax: +49(0)711 68563658 -- 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 -- Dr. Baofu Qiao Institute for Computational Physics Universit�t Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49(0)711 68563607 Fax: +49(0)711 68563658 -- 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 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
[gmx-users] [Fwd: charge group radii]
---BeginMessage--- Hi all, I have recently been testing out the new version of Gromacs. To do so I have used files from previous simulations in Gromacs-4.0.7. When feeding the three files (mdp,gro, and top) into grompp, the following note is displayed: NOTE 3 [file pbc.mdp]: The sum of the two largest charge group radii (0.602793) is larger than rlist (1.50) - rvdw (1.40) This note did not occur in the previous version and it has led to me to ask some questions. 1) I had previously hydrocarbon chains (6-7 carbons long) assigned to individual charge groups, and never any note. Does this mean that my previous simulations have artefacts? (all charge groups have zero net charge) 2) If I am happy with the values of rlist and rvdw, will it not be pretty difficult to assign a charge group with radius 0.1nm? Many Thanks Gavin ---End Message--- -- 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] Error while using forcefield GROMOS 43a1p
Dear Justin, I am trying to do simulation of a system which contains phosphorylated serine using GROMOS 43a1p forcefield. While running pdb2gmx command, I am getting following error. Fatal error: Atom N not found in residue seq.nr. 1 while adding improper thank you in anticipation. With regards, Jignesh Patel -- 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: Failed to lock: pre.log (Gromacs 4.5.3)
Baofu, what operating system are you using? On what file system do you try to store the log file? The error (should) mean that the file system you use doesn't support locking of files. Try to store the log file on some other file system. If you want you can still store the (large) trajectory files on the same file system. Roland On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiao qia...@gmail.com wrote: Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories! Can anyone find the reason causing such error? regards, Baofu Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: Hi, as a workaround you could run with -noappend and later concatenate the output files. Then you should have no problems with locking. Carsten On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of Function not implemented? Any suggestion is appreciated! * Getting Loaded... Reading file pre.tpr, VERSION 4.5.3 (single precision) Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010 --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 1750 Fatal error: Failed to lock: pre.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Doesn't Have to Be Tip Top (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 64 gcq#147: It Doesn't Have to Be Tip Top (Pulp Fiction) -- 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. -- -- mpiexec has exited due to process rank 0 with PID 32758 on -- 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 -- Dr. Baofu Qiao Institute for Computational Physics Universität Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49(0)711 68563607 Fax: +49(0)711 68563658 -- 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] PR
I have read that SPC/SPCE is an rigid and pre-equilibrated 3 point water model. Is it likely mean that position restrained dynamics is not required. If we are not intersted in position restrained dynamics then what are the criteria for system needed. -- Pawan -- 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] PR
Quoting pawan raghav pwnr...@gmail.com: I have read that SPC/SPCE is an rigid and pre-equilibrated 3 point water model. Is it likely mean that position restrained dynamics is not required. As soon as you introduce a protein or anything else, this is no longer true. If we are not intersted in position restrained dynamics then what are the criteria for system needed. Equilibration is successful when the physical observables of interest have converged. Without restraints, the protein structure can be subjected to artifactual forces imparted by solvent reorganization. -Justin -- Pawan 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: Failed to lock: pre.log (Gromacs 4.5.3)
Hi Roland, Thanks a lot! OS: Scientific Linux 5.5. But the system to store data is called as WORKSPACE, different from the regular hardware system. Maybe this is the reason. I'll try what you suggest! regards, Baofu Qiao On 11/26/2010 04:07 PM, Roland Schulz wrote: Baofu, what operating system are you using? On what file system do you try to store the log file? The error (should) mean that the file system you use doesn't support locking of files. Try to store the log file on some other file system. If you want you can still store the (large) trajectory files on the same file system. Roland On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiao qia...@gmail.com wrote: Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories! Can anyone find the reason causing such error? regards, Baofu Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: Hi, as a workaround you could run with -noappend and later concatenate the output files. Then you should have no problems with locking. Carsten On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of Function not implemented? Any suggestion is appreciated! * Getting Loaded... Reading file pre.tpr, VERSION 4.5.3 (single precision) Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010 --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 1750 Fatal error: Failed to lock: pre.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Doesn't Have to Be Tip Top (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 64 gcq#147: It Doesn't Have to Be Tip Top (Pulp Fiction) -- 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. -- -- mpiexec has exited due to process rank 0 with PID 32758 on -- 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] Re: Failed to lock: pre.log (Gromacs 4.5.3)
Hi Baofu, could you provide more information about the file system? The command mount provides the file system used. If it is a network-file-system than the operating system and file system used on the file server is also of interest. Roland On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiao qia...@gmail.com wrote: Hi Roland, Thanks a lot! OS: Scientific Linux 5.5. But the system to store data is called as WORKSPACE, different from the regular hardware system. Maybe this is the reason. I'll try what you suggest! regards, Baofu Qiao On 11/26/2010 04:07 PM, Roland Schulz wrote: Baofu, what operating system are you using? On what file system do you try to store the log file? The error (should) mean that the file system you use doesn't support locking of files. Try to store the log file on some other file system. If you want you can still store the (large) trajectory files on the same file system. Roland On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiao qia...@gmail.com wrote: Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories! Can anyone find the reason causing such error? regards, Baofu Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: Hi, as a workaround you could run with -noappend and later concatenate the output files. Then you should have no problems with locking. Carsten On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of Function not implemented? Any suggestion is appreciated! * Getting Loaded... Reading file pre.tpr, VERSION 4.5.3 (single precision) Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010 --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 1750 Fatal error: Failed to lock: pre.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Doesn't Have to Be Tip Top (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 64 gcq#147: It Doesn't Have to Be Tip Top (Pulp Fiction) -- 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. -- -- mpiexec has exited due to process rank 0 with PID 32758 on -- 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
Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)
Hi Roland, The output of mount is : /dev/mapper/grid01-root on / type ext3 (rw) proc on /proc type proc (rw) sysfs on /sys type sysfs (rw) devpts on /dev/pts type devpts (rw,gid=5,mode=620) /dev/md0 on /boot type ext3 (rw) tmpfs on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) 172.30.100.254:/home on /home type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.254) 172.30.100.210:/opt on /opt type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) 172.30.100.210:/var/spool/torque/server_logs on /var/spool/pbs/server_logs type nfs (ro,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) none on /ipathfs type ipathfs (rw) 172.31.100@o2ib,172.30.100@tcp:172.31.100@o2ib,172.30.100@tcp:/lprod on /lustre/ws1 type lustre (rw,noatime,nodiratime) 172.31.100@o2ib,172.30.100@tcp:172.31.100@o2ib,172.30.100@tcp:/lbm on /lustre/lbm type lustre (rw,noatime,nodiratime) 172.30.100.219:/export/necbm on /nfs/nec type nfs (ro,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219) 172.30.100.219:/export/necbm-home on /nfs/nec/home type nfs (rw,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219) On 11/26/2010 05:41 PM, Roland Schulz wrote: Hi Baofu, could you provide more information about the file system? The command mount provides the file system used. If it is a network-file-system than the operating system and file system used on the file server is also of interest. Roland On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiao qia...@gmail.com wrote: Hi Roland, Thanks a lot! OS: Scientific Linux 5.5. But the system to store data is called as WORKSPACE, different from the regular hardware system. Maybe this is the reason. I'll try what you suggest! regards, Baofu Qiao On 11/26/2010 04:07 PM, Roland Schulz wrote: Baofu, what operating system are you using? On what file system do you try to store the log file? The error (should) mean that the file system you use doesn't support locking of files. Try to store the log file on some other file system. If you want you can still store the (large) trajectory files on the same file system. Roland On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiao qia...@gmail.com wrote: Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories! Can anyone find the reason causing such error? regards, Baofu Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: Hi, as a workaround you could run with -noappend and later concatenate the output files. Then you should have no problems with locking. Carsten On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of Function not implemented? Any suggestion is appreciated! * Getting Loaded... Reading file pre.tpr, VERSION 4.5.3 (single precision) Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010 --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 1750 Fatal error: Failed to lock: pre.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Doesn't Have to Be Tip Top (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 64 gcq#147: It Doesn't Have to Be Tip Top (Pulp Fiction) -- 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
Re: [gmx-users] Thermostat for REMD simulations in implicit solvent
Hi! Have never tried remd with implicit solvent, but note that the unit of tau-t in the mdp-file is ps, not ps-1. This means you should set tau-t = 0.0109 rather than 91. Try this and see if the problem goes away! /Per 26 nov 2010 kl. 15:55 skrev César Ávila clav...@gmail.com: Dear all, I am trying to set up a REMD simulation for a peptide (CHARMM ff) in implicit solvent (OBC GB). Following Bjelkmar et al* I am using stochastics dynamics integration with an inverse friction constant of 91 ps-1, 5 fs timestep, virtual-sites for hydrogens, all-vs-all nonbonded (no cutoff). The full .mdp file is attached at the end of this mail. The problem I am facing is that after a while, the temperatures of all replicas start dropping even below the lowest target temperature. Would you suggest changing some parameter or the whole thermostat to prevent this from happening? @ s0 legend Temperature 0.00 310.811523 5.00 435.627045 10.00 417.161713 15.00 414.248901 20.00 399.390686 25.00 375.087219 30.00 338.131256 35.00 339.961151 40.00 319.424561 45.00 290.442322 50.00 289.587921 55.00 248.746246 60.00 253.192047 65.00 242.619476 70.00 256.051941 75.00 237.648468 80.00 231.938690 85.00 217.029953 90.00 211.447983 95.00 210.393890 100.00 208.518417 105.00 196.718445 110.00 219.245682 115.00 202.957993 120.00 193.128159 125.00 198.278198 130.00 175.304108 135.00 164.925613 140.00 195.024490 145.00 201.153046 150.00 211.160797 155.00 189.525085 160.00 191.156006 165.00 186.545242 170.00 186.885422 175.00 182.838486 180.00 174.960098 185.00 175.244049 190.00 179.517975 195.00 165.785416 200.00 189.871048 205.00 179.510178 210.00 152.527710 215.00 160.109955 220.00 163.564148 * Implementation of the CHARMM ff in GROMACS (2010) JCTC, 6, 459-466 ; Run parameters integrator = sd dt = 0.005; ps ! nsteps = 2 nstcomm = 1 comm_mode = angular ; non-periodic system ; Bond parameters constraints = all-bonds constraint_algorithm= lincs lincs-iter = 1 lincs-order = 6 ; required cutoffs for implicit nstlist = 0 ns_type = grid rlist = 0 rcoulomb= 0 rvdw= 0 epsilon_rf = 0 rgbradii= 0 ; cutoffs required for qq and vdw coulombtype = cut-off vdwtype = cut-off ; temperature coupling tcoupl = v-rescale tc-grps = system tau-t = 91 ref-t = 300 ; Pressure coupling is off Pcoupl = no ; Periodic boundary conditions are off for implicit pbc = no ; Settings for implicit solvent implicit_solvent= GBSA gb_algorithm= OBC gb_epsilon_solvent = 78.3 sa_surface_tension = 2.25936 ;Output control nstxout = 1000 nstfout = 0 nstvout = 0 nstxtcout = 0 nstlog = 1000 nstcalcenergy = -1 nstenergy = 1000 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1993 -- 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] Thermostat for REMD simulations in implicit solvent
I also noticed this error on my setup, so I changed tau-t to 0.1, which is commonly found on others setup. tau-t = 0.0109 seems too low. 2010/11/26 Per Larsson per.lars...@sbc.su.se Hi! Have never tried remd with implicit solvent, but note that the unit of tau-t in the mdp-file is ps, not ps-1. This means you should set tau-t = 0.0109 rather than 91. Try this and see if the problem goes away! /Per 26 nov 2010 kl. 15:55 skrev César Ávila clav...@gmail.com: Dear all, I am trying to set up a REMD simulation for a peptide (CHARMM ff) in implicit solvent (OBC GB). Following Bjelkmar et al* I am using stochastics dynamics integration with an inverse friction constant of 91 ps-1, 5 fs timestep, virtual-sites for hydrogens, all-vs-all nonbonded (no cutoff). The full .mdp file is attached at the end of this mail. The problem I am facing is that after a while, the temperatures of all replicas start dropping even below the lowest target temperature. Would you suggest changing some parameter or the whole thermostat to prevent this from happening? @ s0 legend Temperature 0.00 310.811523 5.00 435.627045 10.00 417.161713 15.00 414.248901 20.00 399.390686 25.00 375.087219 30.00 338.131256 35.00 339.961151 40.00 319.424561 45.00 290.442322 50.00 289.587921 55.00 248.746246 60.00 253.192047 65.00 242.619476 70.00 256.051941 75.00 237.648468 80.00 231.938690 85.00 217.029953 90.00 211.447983 95.00 210.393890 100.00 208.518417 105.00 196.718445 110.00 219.245682 115.00 202.957993 120.00 193.128159 125.00 198.278198 130.00 175.304108 135.00 164.925613 140.00 195.024490 145.00 201.153046 150.00 211.160797 155.00 189.525085 160.00 191.156006 165.00 186.545242 170.00 186.885422 175.00 182.838486 180.00 174.960098 185.00 175.244049 190.00 179.517975 195.00 165.785416 200.00 189.871048 205.00 179.510178 210.00 152.527710 215.00 160.109955 220.00 163.564148 * Implementation of the CHARMM ff in GROMACS (2010) JCTC, 6, 459-466 ; Run parameters integrator = sd dt = 0.005; ps ! nsteps = 2 nstcomm = 1 comm_mode = angular ; non-periodic system ; Bond parameters constraints = all-bonds constraint_algorithm= lincs lincs-iter = 1 lincs-order = 6 ; required cutoffs for implicit nstlist = 0 ns_type = grid rlist = 0 rcoulomb= 0 rvdw= 0 epsilon_rf = 0 rgbradii= 0 ; cutoffs required for qq and vdw coulombtype = cut-off vdwtype = cut-off ; temperature coupling tcoupl = v-rescale tc-grps = system tau-t = 91 ref-t = 300 ; Pressure coupling is off Pcoupl = no ; Periodic boundary conditions are off for implicit pbc = no ; Settings for implicit solvent implicit_solvent= GBSA gb_algorithm= OBC gb_epsilon_solvent = 78.3 sa_surface_tension = 2.25936 ;Output control nstxout = 1000 nstfout = 0 nstvout = 0 nstxtcout = 0 nstlog = 1000 nstcalcenergy = -1 nstenergy = 1000 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1993 -- 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 -- 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
Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 To make things short. The used file system is lustre. /Flo On 11/26/2010 05:49 PM, Baofu Qiao wrote: Hi Roland, The output of mount is : /dev/mapper/grid01-root on / type ext3 (rw) proc on /proc type proc (rw) sysfs on /sys type sysfs (rw) devpts on /dev/pts type devpts (rw,gid=5,mode=620) /dev/md0 on /boot type ext3 (rw) tmpfs on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) 172.30.100.254:/home on /home type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.254) 172.30.100.210:/opt on /opt type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) 172.30.100.210:/var/spool/torque/server_logs on /var/spool/pbs/server_logs type nfs (ro,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) none on /ipathfs type ipathfs (rw) 172.31.100@o2ib,172.30.100@tcp:172.31.100@o2ib,172.30.100@tcp:/lprod on /lustre/ws1 type lustre (rw,noatime,nodiratime) 172.31.100@o2ib,172.30.100@tcp:172.31.100@o2ib,172.30.100@tcp:/lbm on /lustre/lbm type lustre (rw,noatime,nodiratime) 172.30.100.219:/export/necbm on /nfs/nec type nfs (ro,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219) 172.30.100.219:/export/necbm-home on /nfs/nec/home type nfs (rw,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219) On 11/26/2010 05:41 PM, Roland Schulz wrote: Hi Baofu, could you provide more information about the file system? The command mount provides the file system used. If it is a network-file-system than the operating system and file system used on the file server is also of interest. Roland On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiao qia...@gmail.com wrote: Hi Roland, Thanks a lot! OS: Scientific Linux 5.5. But the system to store data is called as WORKSPACE, different from the regular hardware system. Maybe this is the reason. I'll try what you suggest! regards, Baofu Qiao On 11/26/2010 04:07 PM, Roland Schulz wrote: Baofu, what operating system are you using? On what file system do you try to store the log file? The error (should) mean that the file system you use doesn't support locking of files. Try to store the log file on some other file system. If you want you can still store the (large) trajectory files on the same file system. Roland On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiao qia...@gmail.com wrote: Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories! Can anyone find the reason causing such error? regards, Baofu Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: Hi, as a workaround you could run with -noappend and later concatenate the output files. Then you should have no problems with locking. Carsten On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of Function not implemented? Any suggestion is appreciated! * Getting Loaded... Reading file pre.tpr, VERSION 4.5.3 (single precision) Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010 --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 1750 Fatal error: Failed to lock: pre.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Doesn't Have to Be Tip Top (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 64 gcq#147: It Doesn't Have to Be Tip Top (Pulp Fiction) -- MPI_ABORT
Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3): SOLVED
Hi all, What Roland said is right! the lustre system causes the problem of lock. Now I copy all the files to a folder of /tmp, then run the continuation. It works! Thanks! regards, $于 2010-11-26 22:53, Florian Dommert 写道: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 To make things short. The used file system is lustre. /Flo On 11/26/2010 05:49 PM, Baofu Qiao wrote: Hi Roland, The output of mount is : /dev/mapper/grid01-root on / type ext3 (rw) proc on /proc type proc (rw) sysfs on /sys type sysfs (rw) devpts on /dev/pts type devpts (rw,gid=5,mode=620) /dev/md0 on /boot type ext3 (rw) tmpfs on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) 172.30.100.254:/home on /home type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.254) 172.30.100.210:/opt on /opt type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) 172.30.100.210:/var/spool/torque/server_logs on /var/spool/pbs/server_logs type nfs (ro,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) none on /ipathfs type ipathfs (rw) 172.31.100@o2ib,172.30.100@tcp:172.31.100@o2ib,172.30.100@tcp:/lprod on /lustre/ws1 type lustre (rw,noatime,nodiratime) 172.31.100@o2ib,172.30.100@tcp:172.31.100@o2ib,172.30.100@tcp:/lbm on /lustre/lbm type lustre (rw,noatime,nodiratime) 172.30.100.219:/export/necbm on /nfs/nec type nfs (ro,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219) 172.30.100.219:/export/necbm-home on /nfs/nec/home type nfs (rw,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219) On 11/26/2010 05:41 PM, Roland Schulz wrote: Hi Baofu, could you provide more information about the file system? The command mount provides the file system used. If it is a network-file-system than the operating system and file system used on the file server is also of interest. Roland On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiaoqia...@gmail.com wrote: Hi Roland, Thanks a lot! OS: Scientific Linux 5.5. But the system to store data is called as WORKSPACE, different from the regular hardware system. Maybe this is the reason. I'll try what you suggest! regards, Baofu Qiao On 11/26/2010 04:07 PM, Roland Schulz wrote: Baofu, what operating system are you using? On what file system do you try to store the log file? The error (should) mean that the file system you use doesn't support locking of files. Try to store the log file on some other file system. If you want you can still store the (large) trajectory files on the same file system. Roland On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiaoqia...@gmail.com wrote: Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories! Can anyone find the reason causing such error? regards, Baofu Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: Hi, as a workaround you could run with -noappend and later concatenate the output files. Then you should have no problems with locking. Carsten On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of Function not implemented? Any suggestion is appreciated! * Getting Loaded... Reading file pre.tpr, VERSION 4.5.3 (single precision) Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010 --- Program mdrun, VERSION 4.5.3 Source code file: checkpoint.c, line: 1750 Fatal error: Failed to lock: pre.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Doesn't Have to Be Tip Top (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 64 gcq#147: It Doesn't Have to Be Tip Top (Pulp Fiction) -- 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
Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3): SOLVED
Hi, we use Lustre too and it doesn't cause any problem. I found this message on the Lustre list: http://lists.lustre.org/pipermail/lustre-discuss/2008-May/007366.html And according to your mount output, lustre on your machine is not mounted with the flock or localflock option. This seems to be the reason for the problem. Thus if you would like to run the simulation directly on lustre you have to ask the sysadmin to mount it with flock or localflock ( I don't recommend localflock. It doesn't guarantee the correct locking). If you would like to have an option to disable the locking than please file a bug report on bugzilla. The reason we lock the logfile is: We want to make sure that only one simulation is appending to the same files. Otherwise the files could get corrupted. This is why the locking is on by default and currently can't be disabled. Roland On Fri, Nov 26, 2010 at 3:17 PM, Baofu Qiao qia...@gmail.com wrote: Hi all, What Roland said is right! the lustre system causes the problem of lock. Now I copy all the files to a folder of /tmp, then run the continuation. It works! Thanks! regards, $于 2010-11-26 22:53, Florian Dommert 写道: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 To make things short. The used file system is lustre. /Flo On 11/26/2010 05:49 PM, Baofu Qiao wrote: Hi Roland, The output of mount is : /dev/mapper/grid01-root on / type ext3 (rw) proc on /proc type proc (rw) sysfs on /sys type sysfs (rw) devpts on /dev/pts type devpts (rw,gid=5,mode=620) /dev/md0 on /boot type ext3 (rw) tmpfs on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) 172.30.100.254:/home on /home type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.254) 172.30.100.210:/opt on /opt type nfs (rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) 172.30.100.210:/var/spool/torque/server_logs on /var/spool/pbs/server_logs type nfs (ro,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210) none on /ipathfs type ipathfs (rw) 172.31.100@o2ib,172.30.100@tcp:172.31.100@o2ib ,172.30.100@tcp:/lprod on /lustre/ws1 type lustre (rw,noatime,nodiratime) 172.31.100@o2ib,172.30.100@tcp:172.31.100@o2ib ,172.30.100@tcp:/lbm on /lustre/lbm type lustre (rw,noatime,nodiratime) 172.30.100.219:/export/necbm on /nfs/nec type nfs (ro,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219) 172.30.100.219:/export/necbm-home on /nfs/nec/home type nfs (rw,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219) On 11/26/2010 05:41 PM, Roland Schulz wrote: Hi Baofu, could you provide more information about the file system? The command mount provides the file system used. If it is a network-file-system than the operating system and file system used on the file server is also of interest. Roland On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiaoqia...@gmail.com wrote: Hi Roland, Thanks a lot! OS: Scientific Linux 5.5. But the system to store data is called as WORKSPACE, different from the regular hardware system. Maybe this is the reason. I'll try what you suggest! regards, Baofu Qiao On 11/26/2010 04:07 PM, Roland Schulz wrote: Baofu, what operating system are you using? On what file system do you try to store the log file? The error (should) mean that the file system you use doesn't support locking of files. Try to store the log file on some other file system. If you want you can still store the (large) trajectory files on the same file system. Roland On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiaoqia...@gmail.com wrote: Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories! Can anyone find the reason causing such error? regards, Baofu Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: Hi, as a workaround you could run with -noappend and later concatenate the output files. Then you should have no problems with locking. Carsten On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote: Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of Function not implemented? Any
[gmx-users] Re: displacement of drug molecule
I am CC'ing the gmx-users list, as I did on the previous message, so please continue the discussion there. sagar barage wrote: Dear sir, As per your suggestion i have design position restrain file for drug but the displacement is occur during position restrained MD plz give me any new suggestion If things are still moving out of place, you're still not properly using this position restraint file. Make sure you're #including the .itp file properly and using the proper define statement in the .mdp file, if necessary. If you want suggestions aside from guessing at what you should be doing, please include relevant sections of your .top indicating how you're applying the posre.itp file and your .mdp file. Consult the following for tips on proper topology organization: http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults -Justin -- Sagar H. Barage sagarbar...@gmail.com mailto:sagarbar...@gmail.com -- 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] free energy perturbation
antonio wrote: Dear gromacs users I am trying to carry out a free energy perturbation to evaluate the difference in binding energy between two inhibitors of the same protein. I have read a lot of post but i did no understand how to create the topology file. have i to write a mixed pdb of the two inhibitors structure modifying the value of beta factor to -1;0,1 for disappearing and rising atoms and than to proceed by pdb2gmx ? Could someone please link a tutorial or a guide to follow. Please see the manual, section 5.7.4 Topologies for free energy calculations, which includes a relevant example of a topology for transforming between two molecules. There have been significant changes to the free energy code since version 3.3.3, when this type of transformation was (almost) completely controlled in the topology, so your mileage may vary. You do not want (or need) a mixed .pdb file. The B-factor field is irrelevant for such applications, and a hybrid structure will probably break pdb2gmx, anyway. -Justin thanks in advance Antonio -- 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] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?
Francesco Oteri wrote: To see if the problem is force-field related, you could try to run the same simulations using amber-ff. If you will find the same results, probably is a software bug. Some Amber parameter sets (Amber94, I think) have issues of being overly helix-friendly, but perhaps other force fields, in general, might make for good comparisons. But then, too, Gromos96 over-stabilizes extended conformations, so buyer beware... Maybe the bug has been introduced in the version 4 when the Domain Decomposition has been introduced. You can check if it is a software problem using the 3.3.3 version. I doubt that would work. There have been many code changes in order to implement CHARMM. If anything, try mdrun -pd to use the old particle decomposition mode, but I would be very hesitant to blindly say that DD might be causing this behavior. -Justin Il 25/11/2010 23:42, sa ha scritto: Dear All, In a previous message (http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html), I described the results obtained with MD performed with the CHARMM27 ff and the chargegrp yes and no options of a peptide in TIP3P water simulated gromacs. Since these results puzzled me a lot, i would like to share with you others results obtained from the gromacs community advices to explain these results. In few words, the context of these simulations. One of my labmate did, 8 months ago (march/april), several simulations of a peptide (25 AA) with the CHARMM27 ff (and CMAP). The peptide is a transmembrane segment (TM) and belongs to a large membrane protein. This TM segment has an initial helical conformation. The simulations were performed in a cubic box filled with app. 14000 TIP3P water (Jorgensen's model) with 2 Cl ions. To construct the topology file of the system, -chargegrp yes with pdb2gmx and the MD were done with the gromacs 4.0.5. For some reasons, he had to left the lab, and my boss asked me to continue his work. When I checked their results, i was very intrigued by these MD results because he found that the peptide keep along all the simulation time (100 ns) its initial helical conformation. This results are not in agreement with circular dichroism experiments which are shown that the same peptide in water has no helix segment and is completely unfold. I am aware that the simulation time is short compared to experiment time scale, however since i haven't seen any unfolding events in this simulation, so I was not very confident about these results. To explain this inconsistency, I have suspected that the error came probably of the use of the default -chargegrp with CHARMM ff in these simulations since i have read several recent threads about the charge groups problems in the CHARMM ff implementation in gromacs. To examine this hypothesis I have done two simulations with last gromacs version (4.5.3) and two top files containing charge groups and no charge groups for the peptide residus. I used the *same* initial pdb file, box size and simulations parameters. The two simulations were carried out during 24 ns in the NPT ensemble with the md.mdp parameters described below after energy minimisation, NVT and NPT equilibration steps. constraints = all-bonds integrator = md nsteps = 1200 ; 24000ps ou 24ns dt = 0.002 nstlist = 10 nstcalcenergy = 10 nstcomm = 10 continuation= no; Restarting after NPT vdw-type= cut-off rvdw= 1.0 rlist = 0.9 coulombtype = PME rcoulomb = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 optimize_fft= yes nstvout = 5 nstxout = 5 nstenergy = 2 nstlog = 5000 ; update log file every 10 ps nstxtcout = 1000 ; frequency to write coordinates to xtc trajectory every 2 ps Tcoupl = nose-hoover tc-grps = Protein Non-Protein tau-t = 0.4 0.4 ref-t = 298 298 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 3.0 compressibility = 4.5e-5 ref_p = 1.0135 gen_vel = no I found that with charge groups, the peptide remains in its initial helical conformation, whereas with no charge group, the peptide unfolds quickly and has a random coil conformation. I have shown these results to my boss but I was not able to explain why we observe these differences between the two simulations. Indeed since i use PME in the MD, chargegroup should not affect the dynamic results (correct ?) . He asked to do others simulations with different versions of gromacs to see if is not a bug with charge group implementation in gromacs. For testing i have done four others MD wit the *same*
Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero
Anirban Ghosh wrote: Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. You haven't indicated your Gromacs version, but assuming you're using something in the 4.x series, you're not specifying the necessary parameters to do any sort of transformation, particularly couple_lambda0 and couple_lambda1. If left at their default values (vdw-q), nothing gets decoupled. -Justin Regards, Anirban -- 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] Phosphorylated Serine in charmm
Yasmine Chebaro wrote: Hello all, I am using charmm ff in Gromacs 4.5.2, everything goes right with standard proteins, but now i want to run a simulation on a protein with a phosphorylated residue. As mentionned in this post http://www.mail-archive.com/gmx-users@gromacs.org/msg35532.html, I changed the rtp and hbd to add a specific section for the phosphorylated amino-acid, having checked the parametres with charmm. I still have the problem in pdb2gmx where it seems like he can't see the new definition and gives me the residue topology database error. The exact error message and what you have added to the .rtp and .hdb files would be very helpful (read: necessary) to give any useful advice. Is there another file where I have to specify the new amino-acids, I search all the files in the charmm directory in gromacs top, but I still can't find another place where amino-acids are defined. You will need to add your residue to residuetypes.dat as well. -Justin Thanks for you help -- 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] Error while using forcefield GROMOS 43a1p
Jignesh Patel wrote: Dear Justin, I am trying to do simulation of a system which contains phosphorylated serine using GROMOS 43a1p forcefield. While running pdb2gmx command, I am getting following error. Fatal error: Atom N not found in residue seq.nr http://seq.nr. 1 while adding improper Well, either the N atom of residue 1 is not present in your .pdb file (in which case you've got a broken structure that needs fixing), or something else is going on. Without seeing the contents of your input coordinate file (just the first residue, really) and your pdb2gmx command line, there's not much help anyone can give you. -Justin thank you in anticipation. With regards, Jignesh Patel -- 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] Free Energy Calculation: dVpot/dlambda is always zero
Hello Justin, Thanks a lot for the reply. Yes, I am using GROAMCS 4.5 and my system consists of two chains of two proteins, a substrate and an inhibitor solvated in water. So can you please tell me what should be the values for: couple-moltypecouple-lambda0couple-intramolThanks a lot again. Regards, Anirban On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. You haven't indicated your Gromacs version, but assuming you're using something in the 4.x series, you're not specifying the necessary parameters to do any sort of transformation, particularly couple_lambda0 and couple_lambda1. If left at their default values (vdw-q), nothing gets decoupled. -Justin Regards, Anirban -- 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 -- 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
