[gmx-users] segmentation fault with mdrun
Dear All I am trying to perform the azide ion in water simulation with Gromacs. I generated to topology file with PRODG server for azide ion and ran the calculations.I got one error at grompp level which was 327 non-matching atom names atom names from azide.top will be used atom names from azide.gro will be ignored I continued with the maxwarn and performed energy minimization which went smoothly.However no sooner I started equilibration in NVT run using mdrun it crashed with segmentation fault. Please help me to locate the error. I went through the previous mails on the mailing list but I could not sort it out. The topology file is : ; Include forcefield parameters #include ffG43a1.itp ;Include azide topology #include azide.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 azide in water [ molecules ] ; Compound#mols SOL 108 AZI 1 and the itp file for azide which I made from PRODG is [ moleculetype ] ; Name nrexcl AZI 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 N 1 AZI N1 1 -1.000 14.0067 2 N 1 AZI N2 12.000 14.0067 3 N 1 AZI N3 1 -1.000 14.0067 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.112 4527362.40.112 4527362.4 ;N2 N1 2 3 20.112 4527362.40.112 4527362.4 ;N2 N3 [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2180.0 41840001.2180.0 41840001.2 ;N1 N2 N3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] segmentation fault with mdrun
On 8/21/12 6:00 AM, Deepak Ojha wrote: Dear All I am trying to perform the azide ion in water simulation with Gromacs. I generated to topology file with PRODG server for azide ion and ran the calculations.I got one error at grompp level which was 327 non-matching atom names atom names from azide.top will be used atom names from azide.gro will be ignored I continued with the maxwarn and performed energy minimization which went smoothly.However no sooner I started equilibration in NVT run using mdrun it crashed with segmentation fault. Please help me to locate the error. I went through the previous mails on the mailing list but I could not sort it out. Don't use -maxwarn unless you know exactly why you're doing it. The fact that you have 327 non-matching names and 327 atoms in the system (108*3 + 3) suggests the contents of your coordinate file do not match that of the topology in terms of the order of the [molecules] section. Likely your azide should be listed first, presumably if you took the coordinate file for this molecule and solvated it. Also beware that PRODRG topologies are notoriously unreliable and that linear molecules should not be constructed in this way (180 degree angles are not stable). See, for instance, the following tutorial for a more robust method: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html -Justin The topology file is : ; Include forcefield parameters #include ffG43a1.itp ;Include azide topology #include azide.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 azide in water [ molecules ] ; Compound#mols SOL 108 AZI 1 and the itp file for azide which I made from PRODG is [ moleculetype ] ; Name nrexcl AZI 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 N 1 AZI N1 1 -1.000 14.0067 2 N 1 AZI N2 12.000 14.0067 3 N 1 AZI N3 1 -1.000 14.0067 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.112 4527362.40.112 4527362.4 ;N2 N1 2 3 20.112 4527362.40.112 4527362.4 ;N2 N3 [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2180.0 41840001.2180.0 41840001.2 ;N1 N2 N3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] Segmentation fault after mdrun for MD simulation
Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.048739, max 1.100685 (between atoms 8422 and 8421) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length .. .. snip .. .. starting mdrun 'TUBULIN ALPHA CHAIN' 25000 steps, 50.0 ps. Warning: 1-4 interaction between 8443 and 8446 at distance 2.853 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size .. .. snip .. .. step 0: Water molecule starting at atom 23781 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.1# Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1# Back Off! I just backed up step0b_n5.pdb to ./#step0b_n5.pdb.2# Back Off! I just backed up step0b_n3.pdb to ./#step0b_n3.pdb.2# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.1# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1# Back Off! I just backed up step0c_n5.pdb to ./#step0c_n5.pdb.2# Back Off! I just backed up step0c_n3.pdb to ./#step0c_n3.pdb.2# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates ^Mstep 0/opt/sge/jacobson/spool/node-2-05/job_scripts/1097116: line 21: 1473 Segmentation fault (core dumped) $MDRUN -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s 1JFF_md.tpr -o 1JFF_md.trr -c 1JFF_pmd.gro -x 1JFF_md.xtc -e 1JFF_md.edr On 16 August 2011 10:58, Justin A. Lemkul jalem...@vt.edu wrote: rainy908 wrote: Hi, I get the error Atomtype CR1 not found when I execute grompp. After perusing the gmx archives, I understand this error has to do with the lack of CR1 being specified in the force field. However, I did include the appropriate .itp files in my .top file (shown below). As you can see, obviously CR1 is specified in taxol.itp and gtp.itp. Therefore, I'm not sure what exactly is the problem here. You're mixing and matching force fields.
Re: [gmx-users] Segmentation fault after mdrun for MD simulation
rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length If mdrun is failing at step 0, it indicates that your system is physically unreasonable. Either the starting configuration has atomic clashes that have not been resolved (and thus you need better EM and/or equilibration) or that the parameters assigned to the molecules in your system are unreasonable. -Justin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.048739, max 1.100685 (between atoms 8422 and 8421) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length .. .. snip .. .. starting mdrun 'TUBULIN ALPHA CHAIN' 25000 steps, 50.0 ps. Warning: 1-4 interaction between 8443 and 8446 at distance 2.853 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size .. .. snip .. .. step 0: Water molecule starting at atom 23781 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.1# Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1# Back Off! I just backed up step0b_n5.pdb to ./#step0b_n5.pdb.2# Back Off! I just backed up step0b_n3.pdb to ./#step0b_n3.pdb.2# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.1# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1# Back Off! I just backed up step0c_n5.pdb to ./#step0c_n5.pdb.2# Back Off! I just backed up step0c_n3.pdb to ./#step0c_n3.pdb.2# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates ^Mstep 0/opt/sge/jacobson/spool/node-2-05/job_scripts/1097116: line 21: 1473 Segmentation fault (core dumped) $MDRUN -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s 1JFF_md.tpr -o 1JFF_md.trr -c 1JFF_pmd.gro -x 1JFF_md.xtc -e 1JFF_md.edr On 16 August 2011 10:58, Justin A. Lemkul jalem...@vt.edu wrote: rainy908 wrote: Hi, I get the error Atomtype CR1 not found when I execute grompp. After perusing the gmx archives, I
Re: [gmx-users] Segmentation fault after mdrun for MD simulation
Hi Justin, THanks for the input. So I traced back to my energy minimization steps, and am getting the error message after I execute the following line: $mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr output: Back Off! I just backed up md.log to ./#md.log.2# Reading file 1JFF_em.tpr, VERSION 4.5.3 (single precision) Starting 24 threads Will use 15 particle-particle and 9 PME only nodes This is a guess, check the performance at the end of the log file --- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 15 nodes that is compatible with the given box and a minimum cell size of 2.92429 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I figure the problem must lie within my em.mdp file: title = 1JFF cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.001 ; ps ! nsteps = 1 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 ~ I figure this is an issue related to with PME and the Fourier spacing? Thanks, rainy908 On 17 August 2011 17:55, Justin A. Lemkul jalem...@vt.edu wrote: rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length If mdrun is failing at step 0, it indicates that your system is physically unreasonable. Either the starting
Re: [gmx-users] Segmentation fault after mdrun for MD simulation
On 18/08/2011 2:41 PM, rainy908 wrote: Hi Justin, THanks for the input. So I traced back to my energy minimization steps, and am getting the error message after I execute the following line: $mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr output: Back Off! I just backed up md.log to ./#md.log.2# Reading file 1JFF_em.tpr, VERSION 4.5.3 (single precision) Starting 24 threads Will use 15 particle-particle and 9 PME only nodes This is a guess, check the performance at the end of the log file --- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 15 nodes that is compatible with the given box and a minimum cell size of 2.92429 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I figure the problem must lie within my em.mdp file: It could, but if you follow the above advice you will learn about some other considerations. Mark title = 1JFF cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.001 ; ps ! nsteps = 1 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 ~ I figure this is an issue related to with PME and the Fourier spacing? Thanks, rainy908 On 17 August 2011 17:55, Justin A. Lemkuljalem...@vt.edu wrote: rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30
Re: [gmx-users] segmentation fault after mdrun
On Feb 23, 2009, at 9:22 AM, Nikit sharan wrote: Dear justin, As you suggested i have changed the coloumb type to PME and set pme_order to 5 as said in the mailing list as it will increase the Hi Nikit, I think pme_order should be an even number in gromacs. You might want to try with order = 6 then. Carsten -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 after mdrun
Nikit sharan wrote: Dear justin, As you suggested i have changed the coloumb type to PME and set pme_order to 5 as said in the mailing list as it will increase the Try an even number. accuracy.But then the simulation is not getting completed.Its taking hours together.Normally what's the running time for a lipid bilayer?I Timings will be dependent on your hardware, especially the communication between nodes in a cluster. -Justin dint find anything wrong with the topology as it is downloaded from tielman's website.it is also well equilibriated.Kindly give me your suggestions.My mdp.file is below: title= Yo cpp = cpp include = define = integrator = md tinit= 0 dt = 0.005 nsteps = 5 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= system nstxout = 200 nstvout = 0 nstfout = 0 nstcheckpoint= 1000 nstlog = 100 nstenergy= 100 nstxtcout= 1000 xtc-precision= 1000 nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 0.5 0.5 0.5 compressibility = 4.5e-5 4.5e-5 4.5e-5 ref_p= 1.0 1.0 1.0 andersen_seed= 815131 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Graduate Research Assistant 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://www.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] segmentation fault after mdrun
Hello sir, Thanks for your suggestion.Then as u suggested i start the work from scratch and did the equilibriation again, there is nothing wrong with the topology also because it was taken from tiemann's website.The only message that it gives after equlibriation run is Steepest Descents converged to machine precision in 159 steps, but did not reach the requested Fmax 1e-05. Potential Energy = -3.3737231e+05 Maximum force = 2.6356035e+03 on atom 4665 Norm of force = 1.2290095e+04 do i have to upgrade to double precision for simuating dppc bilayer?but many of them worked fine with single precision alone. When i proceded with the production run, again either its not giving run with 5 steps or when i reduced step from 5 to 50 to check what's the output then it gives me an error saying Warning: pressure scaling more than 1%, mu: 1.12479 1.12479 1.00476 Back Off! I just backed up step7018.pdb to ./#step7018.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault since its giving an error with pressure scaling, the parameter that i need to adjust is ref_p??by default i said that to 1.0?Now what value i have to change. I willl be really thanful if you have a look at the segmentation fault also. title= Yo cpp = cpp include = define = integrator = md tinit= 0 dt = 0.005 nsteps = 5 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= system nstxout = 200 nstvout = 0 nstfout = 0 nstcheckpoint= 1000 nstlog = 100 nstenergy= 100 nstxtcout= 1000 xtc-precision= 1000 nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 domain-decomposition = no coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1.0 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 0.5 0.5 0.5 compressibility = 4.5e-5 4.5e-5 4.5e-5 ref_p= 1.0 1.0 1.0 andersen_seed= 815131 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 after mdrun
Nikit sharan wrote: Hello sir, Thanks for your suggestion.Then as u suggested i start the work from scratch and did the equilibriation again, there is nothing wrong with the topology also because it was taken from tiemann's website.The only message that it gives after equlibriation run is Steepest Descents converged to machine precision in 159 steps, but did not reach the requested Fmax 1e-05. Potential Energy = -3.3737231e+05 Maximum force = 2.6356035e+03 on atom 4665 Norm of force = 1.2290095e+04 do i have to upgrade to double precision for simuating dppc bilayer?but many of them worked fine with single precision alone. I would guess not. 1e-5 is an extremely small Fmax. Why are you using that value? When i proceded with the production run, again either its not giving run with 5 steps or when i reduced step from 5 to 50 to check what's the output then it gives me an error saying Warning: pressure scaling more than 1%, mu: 1.12479 1.12479 1.00476 Back Off! I just backed up step7018.pdb to ./#step7018.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault since its giving an error with pressure scaling, the parameter that i need to adjust is ref_p??by default i said that to 1.0?Now what value i have to change. Probably this is a symptom of the problem, not the problem itself. See http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25 I willl be really thanful if you have a look at the segmentation fault also. Segmentation fault just indicates some catastrophic failure. title= Yo cpp = cpp include = define = integrator = md tinit= 0 dt = 0.005 See the final line of the above link. nsteps = 5 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= system nstxout = 200 nstvout = 0 nstfout = 0 nstcheckpoint= 1000 nstlog = 100 nstenergy= 100 nstxtcout= 1000 xtc-precision= 1000 nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 domain-decomposition = no coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1.0 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 0.5 0.5 0.5 compressibility = 4.5e-5 4.5e-5 4.5e-5 ref_p= 1.0 1.0 1.0 andersen_seed= 815131 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 after mdrun
Mark Abraham wrote: coulombtype = Cut-off In addition to everything Mark said, you should also *never* run a bilayer simulation with a simply cutoff scheme. You will get terrible artefacts. That goes for most other simulations too, but it has been demonstrated very recently for bilayers that one should always use PME. -Justin Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Graduate Research Assistant 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://www.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 : RE : [gmx-users] segmentation fault in mdrun when using PME
It seems that in my case this is a bug (see Bugzilla, bug # 74) related to using the Intel Math Kernel Library (MKL) v. 8.0.1 for Fourier transforms. The team managing the Altix are trying different FFT libraries. Eric Lindahl says that using a FFT library that is not optimized for Itanium 2 shouldn't hamper the perfomance very much since FT doesn't represent a very big part of the computation. I think the error I get with the version compiled without Fortran is boggus, because this tutorial (John Kerrigan's) was tried sucessfully by many people, so there shouldn't be any mistakes in the .mdp file. Also, the runs I do with that version have strange output and anyway, I don't get that error with the Fortran-enabled version. Segmentation fault has been documented in the position restrained dynamics stage of this tutorial with gromacs 3.3.0 though, and was solved when upgrading to 3.3.1. An exploding system is often caused by extreme forces due to bad contacts, which can be relieved by a minimization step. Have you used a steepest descents minimization step on your system before doing the pr ? De: [EMAIL PROTECTED] de la part de Arneh Babakhani Date: mar. 2006-05-02 23:21 À: Discussion list for GROMACS users Objet : Re: RE : [gmx-users] segmentation fault in mdrun when using PME Hello, I'm experiencing the exact same problem, when trying to do some restrained molecular dynamics of a small peptide in a water box. Have you had any luck in trouble-shooting this? (I've pasted my mdp file below, for your reference). Also running Gromacs 3.3.1 Arneh title = ResMD warnings = 10 cpp = /usr/bin/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 25000 ; total 50.0 ps. nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein sol ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Diane Fournier wrote: De: [EMAIL PROTECTED] de la part de David van der Spoel Date: lun. 2006-05-01 13:33 À: Discussion list for GROMACS users Objet : Re: [gmx-users] segmentation fault in mdrun when using PME Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). Still doesn't work. logfile ends in the usual way. Except this time, I get this output: Reading file trp_em.tpr, VERSION 3.3.1 (single precision) Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 500 Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Wrote pdb files with previous and current coordinates and then these files get written: step0.pdb #step0.pdb.1# step-1.pdb step1.pdb Will file a bugzilla. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx
RE: [gmx-users] segmentation fault in mdrun when using PME
-Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cutoff instead of PME. I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel Itanium 2 processors (but I'm currently using a single node, so it's not a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized for Itanium 2). the em.mdp file looks like: title = drg_trp cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Is it possible this could be related to insufficient memory allocation ? How demanding is this PME calculation ? Not likely a memory problem. It could be a compiler issue but we need more info! Where does it crash? Is it reproducible? DOes the same tpr file cause a crash on another architecture (e.g. your desktop)? I installed gromacs 3.3.1 on my desktop (Pentium 4 under linux fedora core 4 and using the fftw3 fourier transform library). I used the .tpr file generated on the altix in mdrun and it worked fine. When I run that same file on the altix, it crashes every time without any iteration in the .log file: Removing pbc first time Done rmpbc Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 14580 Started Steepest Descents on node 0 Mon May 1 11:47:39 2006 PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- After that the file ends. There is no other error message than segmentation fault with core dump. The compilers that are used on the altix are: C++ Version 99.0-023 - 9.0-031 C++ Version 88.1-033 - 8.1-036 Fortran 99.0-021 - 9.0-032 Fortran 88.1-029 - 8.1-033 IPP 4.1 - 5.0 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] segmentation fault in mdrun when using PME
Diane Fournier wrote: -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cutoff instead of PME. I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel Itanium 2 processors (but I'm currently using a single node, so it's not a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized for Itanium 2). the em.mdp file looks like: title = drg_trp cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Is it possible this could be related to insufficient memory allocation ? How demanding is this PME calculation ? Not likely a memory problem. It could be a compiler issue but we need more info! Where does it crash? Is it reproducible? DOes the same tpr file cause a crash on another architecture (e.g. your desktop)? I installed gromacs 3.3.1 on my desktop (Pentium 4 under linux fedora core 4 and using the fftw3 fourier transform library). I used the .tpr file generated on the altix in mdrun and it worked fine. When I run that same file on the altix, it crashes every time without any iteration in the .log file: Removing pbc first time Done rmpbc Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 14580 Started Steepest Descents on node 0 Mon May 1 11:47:39 2006 PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- After that the file ends. There is no other error message than segmentation fault with core dump. The compilers that are used on the altix are: C++ Version 99.0-023 - 9.0-031 C++ Version 88.1-033 - 8.1-036 Fortran 99.0-021 - 9.0-032 Fortran 88.1-029 - 8.1-033 IPP 4.1 - 5.0 Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] segmentation fault in mdrun when using PME
Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cutoff instead of PME. I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel Itanium 2 processors (but I'm currently using a single node, so it's not a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized for Itanium 2). the em.mdp file looks like: title = drg_trp cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Is it possible this could be related to insufficient memory allocation ? How demanding is this PME calculation ? Not likely a memory problem. It could be a compiler issue but we need more info! Where does it crash? Is it reproducible? DOes the same tpr file cause a crash on another architecture (e.g. your desktop)? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] segmentation fault in mdrun when using PME
Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan'sDrug-Enzyme tutorial and mdrun crashes withsegmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cutoff instead of PME. I'm working withGromacs v. 3.3.1on a SGI altix 3700 with 32 Intel Itanium2 processors (but I'm currently using a single node, so it's not a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel Math Kernel Librarary (MKL) v. 8.0.1 as FFT library(which is optimized for Itanium 2). the em.mdp file looks like: title = drg_trpcpp = /usr/bin/cppdefine = -DFLEX_SPCconstraints = noneintegrator = steepdt = 0.002 ; ps !nsteps = 500nstlist = 10ns_type = gridrlist = 0.9coulombtype = PMErcoulomb = 0.9rvdw = 0.9fourierspacing = 0.12fourier_nx = 0fourier_ny = 0fourier_nz = 0pme_order = 4ewald_rtol = 1e-5optimize_fft = yes;; Energy minimizing stuff;emtol = 1000.0emstep = 0.01 Is it possible this could be related to insufficient memory allocation ? How demanding is this PME calculation ? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
