Re: [gmx-users] trajectory output from g_select ?
Ok, I'll try the python solution Thanks for your help, Jonathan -- 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] Vectors in non-cubic box
Hi, I want to create *.gro file with simulation box size as following: 3.460467452 0. 0. 1.730233726 2.9968527222000 0. 0. 0. 10.00 I used the command: ]editconf –f *.pdb –o *.gro –box 3.46 3.46 10.–c–angle 90 90 60 are these commands proper to create this simulation box size? system size : 4.975 2.951 0.084 (nm) center : 0.025 0.548 0.966 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 2.570 0.951 4.034 (nm) new center : 2.595 1.498 5.000 (nm) new box vectors : 3.460 3.460 10.000 (nm) new box angles : 90.00 90.00 60.00 (degrees) new box volume : 103.68 (nm^3) Also I paste some .gro file 1 NAU 39 1.759 1.647 4.998 1 HAC 41 1.855 1.618 4.993 1 HAB 40 1.686 1.578 5.002 3.46000 2.99645 10.0 0.0 0.0 1.73000 0. -0. -0.0 What is three last values in box vector,0.00 -0.00 -.0 0? Would one please clear me about these vectors? 3.46000 2.99645 10.0 0.0 0.0 1.73000 0. -0. -0.0 xx yy zz ? ? xy ?? ? I have another question that does g_hbond has the compatibility with non-cubic (or parallelpiped) cells? good luck Afsaneh -- 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] Vectors in non-cubic box
Hi Afsaneh, The PBC and the .gro file format are explained in the manual, chapter 3. The last line of the .gro file has the box stored as XX YY ZZ XY XZ YX YZ ZX ZY Cheers, Tsjerk On Mar 5, 2011 6:03 AM, "afsaneh maleki" wrote: Hi, I want to create *.gro file with simulation box size as following: 3.460467452 0. 0. 1.730233726 2.9968527222000 0. 0. 0. 10.00 I used the command: ]editconf –f *.pdb –o *.gro –box 3.46 3.46 10.–c–angle 90 90 60 are these commands proper to create this simulation box size? system size : 4.975 2.951 0.084 (nm) center : 0.025 0.548 0.966 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 2.570 0.951 4.034 (nm) new center : 2.595 1.498 5.000 (nm) new box vectors : 3.460 3.460 10.000 (nm) new box angles : 90.00 90.00 60.00 (degrees) new box volume : 103.68 (nm^3) Also I paste some .gro file 1 NAU 39 1.759 1.647 4.998 1 HAC 41 1.855 1.618 4.993 1 HAB 40 1.686 1.578 5.002 3.46000 2.99645 10.0 0.0 0.0 1.73000 0. -0. -0.0 What is three last values in box vector,0.00 -0.00 -.0 0? Would one please clear me about these vectors? 3.46000 2.99645 10.0 0.0 0.0 1.73000 0. -0. -0.0 xx yy zz ? ? xy ?? ? I have another question that does g_hbond has the compatibility with non-cubic (or parallelpiped) cells? good luck Afsaneh -- 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] Vectors in non-cubic box
Thanks Dear Tsjerk g_hbond has the compatibility with non-cubic (or parallelpiped) cells? Best wishes, Afsaneh -- 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] Vectors in non-cubic box
Hi Afsaneh, Sorry for missing out on that one. Yes, all tools properly deal with tric. cells. Cheers, Tsjerk On Mar 5, 2011 7:24 AM, "afsaneh maleki" wrote: Thanks Dear Tsjerk g_hbond has the compatibility with non-cubic (or parallelpiped) cells? Best wishes, Afsaneh -- 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] mdrun-gpu
Dear Natalia, The current mdrun-gpu (which btw uses OpenMM) is capable to run a single simulation, on a single node, using a single GPU only. Cheers, -- Szilárd On Fri, Mar 4, 2011 at 6:28 PM, Nathalia Garces wrote: > Hello, > I want to know if it is possible to use "mdrun-gpu" with the command > "-multi", meaning to use GPUs using paralell simulation. > When I used it (mdrun-gpu -multi 2 -replex 2 ), it appears me an error shown > bellow > Fatal error: > This binary is compiled without MPI support, can not do multiple > simulations. > > this bewilder me because I'm not sure I can use gpu and mpi at the same > time. > > > Thank you for four answer > > Nathalia > > -- > gmx-users mailing list gmx-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] Warning: 1-4 interaction
Hi everyone, My attempt to conduct a NPT failed although everything seemed to be going well. Topology is OK and I am just curious why system is blowing up all of a sudden towards the end of simulation. I should mention that by changing fourierspacing from 0.12 to 0.3 everything works fine till the end of run and comparison between energy terms (up until the crash point) shows very slight difference between two runs ( less than 2% even for electrostatic terms). I am aware that blowing up is due to unphysical forces but is this happening by accidient or there is an underlying reason I should take care of. Thanks, Best, Moeed step 164300, remaining runtime: 241 s step 164400, remaining runtime: 240 s step 164500, remaining runtime: 240 s step 164600, remaining runtime: 239 s Warning: 1-4 interaction between 260 and 267 at distance 73679654.990 which is larger than the 1-4 table size 2.250 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 = results till t=320 ps (before first run crash) fourierspacing = 0.12 LJ-14 757.24626.623926.5661 -0.0189929 -6.0 Coulomb-14 -186.50915.986615.9529 -0.0112174 -3.5896 LJ (SR)-2691.84117.026107.231 -0.507373 -162.361 Coulomb (SR)725.66217.648317.5876 0.0158275 5.06483 fourierspacing = 0.3 LJ-14 757.12926.493626.4578 -0.0149128 -4.77214 Coulomb-14 -199.523 14.949 14.158 -0.0519427 -16.6218 LJ (SR) -2670.5111.201109.6880.19784 63.3092 Coulomb (SR)739.79416.180715.4473 0.0521352 16.6834 pbc = xyz ;Run control integrator = md dt = 0.002 nsteps = 100 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.25 rcoulomb= 1.25 ;1.1 rvdw= 1.0 ;PME parameters fourierspacing = 0.3 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;Temperature coupling Tcoupl = v-rescale tc-grps = System ;HEX tau_t = 0.1 ;0.1 ref_t = 400 ;300 ;Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 ;0.5 compressibility = 4.5e-5 4.5e-5 ref_p = 7070 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs -- 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] Warning: 1-4 interaction
Moeed wrote: Hi everyone, My attempt to conduct a NPT failed although everything seemed to be going well. Topology is OK and I am just curious why system is blowing up all of a sudden towards the end of simulation. I should mention that by changing fourierspacing from 0.12 to 0.3 everything works fine till the end of run and comparison between energy terms (up until the crash point) shows very slight difference between two runs ( less than 2% even for electrostatic terms). I am aware that blowing up is due to unphysical forces but is this happening by accidient or there is an underlying reason I should take care of. Everything has a cause; nothing is accidental. No stable run should ever show LINCS warnings like this, so yes, there is something to fix. You also have not proven that your fourierspacing is not the cause. The proper term to analyze is Coul-recip, which corresponds to reciprocal space Coulombic term. I don't see that listed below. -Justin Thanks, Best, Moeed step 164300, remaining runtime: 241 s step 164400, remaining runtime: 240 s step 164500, remaining runtime: 240 s step 164600, remaining runtime: 239 s Warning: 1-4 interaction between 260 and 267 at distance 73679654.990 which is larger than the 1-4 table size 2.250 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 = results till t=320 ps (before first run crash) fourierspacing = 0.12 LJ-14 757.24626.623926.5661 -0.0189929 -6.0 Coulomb-14 -186.50915.986615.9529 -0.0112174 -3.5896 LJ (SR)-2691.84117.026107.231 -0.507373 -162.361 Coulomb (SR)725.66217.648317.5876 0.0158275 5.06483 fourierspacing = 0.3 LJ-14 757.12926.493626.4578 -0.0149128 -4.77214 Coulomb-14 -199.523 14.949 14.158 -0.0519427 -16.6218 LJ (SR) -2670.5111.201109.6880.19784 63.3092 Coulomb (SR)739.79416.180715.4473 0.0521352 16.6834 pbc = xyz ;Run control integrator = md dt = 0.002 nsteps = 100 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.25 rcoulomb= 1.25 ;1.1 rvdw= 1.0 ;PME parameters fourierspacing = 0.3 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;Temperature coupling Tcoupl = v-rescale tc-grps = System ;HEX tau_t = 0.1 ;0.1 ref_t = 400 ;300 ;Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 ;0.5 compressibility = 4.5e-5 4.5e-5 ref_p = 7070 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs -- 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
Re: [gmx-users] Warning: 1-4 interaction
On 06/03/11, Moeed wrote: > Hi everyone, > > My attempt to conduct a NPT failed although everything seemed to be going > well. Topology is OK and I am just curious why system is blowing up all of a > sudden towards the end of simulation. I should mention that by changing > fourierspacing from 0.12 to 0.3 everything works fine till the end of run and > comparison between energy terms (up until the crash point) shows very slight > difference between two runs ( less than 2% even for electrostatic terms). I > am aware that blowing up is due to unphysical forces but is this happening by > accidient or there is an underlying reason I should take care of. > Don't change fourierspacing unless you can measure the error so introduced (which you can't, easily, yet), and can defend the assertion that it does not affect your observations. Generating velocities at the start of an NPT run seems unwise. A better-behaved protocol will equilibrate the velocities under NVT before fixing the density under NPT, before then moving to the production simulation ensemble. Mark > Thanks, > Best, > Moeed > > > step 164300, remaining runtime: 241 s > step 164400, remaining runtime: 240 s > step 164500, remaining runtime: 240 s > > step 164600, remaining runtime: 239 s > > Warning: 1-4 interaction between 260 and 267 at distance 73679654.990 which > is larger than the 1-4 table size 2.250 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 > = > > results till t=320 ps (before first run crash) > fourierspacing = 0.12 > > > > > LJ-14 > 757.246 26.6239 26.5661 -0.0189929 -6.0 > > > > Coulomb-14 > -186.509 15.9866 15.9529 -0.0112174 -3.5896 > > > > LJ (SR) > -2691.84 117.026 107.231 > -0.507373 -162.361 > > > > Coulomb (SR) > 725.662 17.6483 17.5876 > 0.0158275 5.06483 > > > > > > fourierspacing = 0.3 > > > > > > > LJ-14 > 757.129 26.4936 26.4578 -0.0149128 -4.77214 > > > > Coulomb-14 > -199.523 14.949 14.158 -0.0519427 -16.6218 > > > > LJ (SR) > -2670.5 111.201 109.688 > 0.19784 63.3092 > > > > Coulomb (SR) > 739.794 16.1807 15.4473 > 0.0521352 16.6834 > > > > pbc = xyz > > > ; Run control > integrator = md > > > dt = 0.002 > nsteps = 100 ;5000 > nstcomm = 100 > > ; Output control > nstenergy = 100 > > > > > > nstxout = 100 > nstvout = 0 > nstfout = 0 > nstlog = 1000 > nstxtcout = 1000 > > ; Neighbor searching > > > > > > nstlist = 10 > ns_type = grid > > ; Electrostatics/VdW > coulombtype = PME > vdw-type = Shift > > > > > > rcoulomb-switch = 0 > rvdw-switch = 0.9 ;0 > > ; Cut-offs > rlist = 1.25 > rcoulomb = 1.25 ;1.1 > rvdw = 1.0 > > > > > > > ; PME parameters > fourierspacing = 0.3 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > > > > > > optimize_fft = yes > > ; Temperature coupling > Tcoupl = v-rescale > tc-grps = System ;HEX > tau_t = 0.1 ;0.1 > > > > > > ref_t = 400 ;300 > > ; Pressure coupling > Pcoupl = Parrinello-Rahman > Pcoupltype = isotropic > tau_p = 1 1 ;0.5 > > > > > > compressibility = 4.5e-5 4.5e-5 > ref_p = 70 70 > > ; Velocity generation > gen_vel = yes > gen_temp = 300.0 > > > > > > gen_seed = 173529 > > ; Bonds > constraints = all-bonds > constraint-algorithm
Re: [gmx-users] Warning: 1-4 interaction
Hello Justin, I just scanned through the manual and also looked into the list to learn about the significance of reciprocal part to realize your statement. I did not find much about the fact that how I can judge if fourierspacing is the cause of the crash (I mean relevance between fourierspacing and coulb recip). I suspect the cause of crashes is because of electrostatics settings. BEfore that I had only vdw no run crashed. Since I used to get LINCS warning I removed bond constraints but still system is showing instabilities. I am confident that topology is fine and just wondering how else one can inspect root cause for unphysical forces. fourierspacing =0.12 : Coul. recip.636.2178.69433 8.62908 0.01673983.68278 fourierspacing =0.3 :Coul. recip.642.9216.06063 6.02832 -0.00984063 -2.16496 >> > Everything has a cause; nothing is accidental. No stable run should ever > show LINCS warnings like this, so yes, there is something to fix. > > You also have not proven that your fourierspacing is not the cause. The > proper term to analyze is Coul-recip, which corresponds to reciprocal space > Coulombic term. I don't see that listed below. > > -Justin > > > Thanks, >> Best, >> Moeed >> >> >> step 164300, remaining runtime: 241 s step 164400, remaining >> runtime: 240 s step 164500, remaining runtime: 240 s >> step 164600, remaining runtime: 239 s Warning: 1-4 interaction >> between 260 and 267 at distance 73679654.990 which is larger than the 1-4 >> table size 2.250 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 >> = >> results till t=320 ps (before first run crash) >> fourierspacing = 0.12 >> >> LJ-14 757.24626.623926.5661 -0.0189929 >> -6.0 >> >> Coulomb-14 -186.50915.986615.9529 -0.0112174 >> -3.5896 >> >> LJ (SR)-2691.84117.026107.231 -0.507373 >> -162.361 >> >> Coulomb (SR)725.66217.648317.5876 0.0158275 >> 5.06483 >> >> >> fourierspacing = 0.3 >> >> >> LJ-14 757.12926.493626.4578 -0.0149128 >> -4.77214 >> >> Coulomb-14 -199.523 14.949 14.158 -0.0519427 >> -16.6218 >> >> LJ (SR) -2670.5111.201109.6880.19784 >> 63.3092 >> >> Coulomb (SR)739.79416.180715.4473 0.0521352 >> 16.6834 >> >> >> pbc = xyz >> ;Run control integrator = md >> dt = 0.002 nsteps >> = 100 ;5000 nstcomm = 100 >> ;Output control >> nstenergy = 100 nstxout = 100 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 nstxtcout = 1000 >> >> ;Neighbor searching >> nstlist = 10 ns_type = grid >> >> ;Electrostatics/VdW >> coulombtype = PMEvdw-type= Shift >> rcoulomb-switch = 0 rvdw-switch = >> 0.9 ;0 >> ;Cut-offs >> rlist = 1.25 rcoulomb= 1.25 >> ;1.1 rvdw= 1.0 >> ;PME parameters >> fourierspacing = 0.3 fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4ewald_rtol = 1e-5 >> optimize_fft = yes >> >> ;Temperature coupling Tcoupl = v-rescale >> tc-grps = System ;HEX tau_t = >> 0.1 ;0.1 ref_t = 400 ;300 >> >> ;Pressure coupling >> Pcoupl = Parrinello-RahmanPcoupltype = >> isotropic tau_p = 1 1 ;0.5 >> compressibility = 4.5e-5 4.5e-5 ref_p = >> 7070 >> ;Velocity generation gen_vel = yes >> gen_temp= 300.0 gen_seed= >> 173529 >> ;Bonds >> constraints = all-bonds constraint-algorithm = >> lincs >> >> > -- > > > 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 > > ===
Re: [gmx-users] Warning: 1-4 interaction
Moeed wrote: Hello Justin, I just scanned through the manual and also looked into the list to learn about the significance of reciprocal part to realize your statement. I did not find much about the fact that how I can judge if fourierspacing is the cause of the crash (I mean relevance between fourierspacing and coulb recip). I suspect the cause of crashes is because of The manual will not describe every detail, but an understanding of the algorithms (through reading the appropriate literature) should provide you with what you need. Take Mark's advice and leave fourierspacing at its default value unless you are 100% sure of the effects of messing with it. electrostatics settings. BEfore that I had only vdw no run crashed. That was a broken model, as we've discussed. Don't believe that its results are reliable. Since I used to get LINCS warning I removed bond constraints but still LINCS warnings don't mean you should turn off constraints. With a 2-fs timestep and an all-atom model, you absolutely need to be using constraints. http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings system is showing instabilities. I am confident that topology is fine and just wondering how else one can inspect root cause for unphysical forces. The best advice I can give has already been given: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System Watch the trajectory. See what falls apart. You're also applying 70 bar of pressure to a system that may not yet be properly equilibrated for such conditions. I have found that the Parrinello-Rahman barostat is not particularly well-suited to harsh conditions, tight coupling, or simulations of any system that is far from equilibrium. You might be better off with Berendsen (and a fairly long tau_p) until your system stabilizes. -Justin fourierspacing =0.12 : Coul. recip.636.217 8.694338.62908 0.01673983.68278 fourierspacing =0.3 :Coul. recip.642.921 6.060636.02832 -0.00984063 -2.16496 Everything has a cause; nothing is accidental. No stable run should ever show LINCS warnings like this, so yes, there is something to fix. You also have not proven that your fourierspacing is not the cause. The proper term to analyze is Coul-recip, which corresponds to reciprocal space Coulombic term. I don't see that listed below. -Justin Thanks, Best, Moeed step 164300, remaining runtime: 241 s step 164400, remaining runtime: 240 s step 164500, remaining runtime: 240 s step 164600, remaining runtime: 239 s Warning: 1-4 interaction between 260 and 267 at distance 73679654.990 which is larger than the 1-4 table size 2.250 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 = results till t=320 ps (before first run crash) fourierspacing = 0.12 LJ-14 757.24626.623926.5661 -0.0189929 -6.0 Coulomb-14 -186.50915.986615.9529 -0.0112174-3.5896 LJ (SR)-2691.84117.026107.231 -0.507373 -162.361 Coulomb (SR)725.66217.648317.5876 0.01582755.06483 fourierspacing = 0.3 LJ-14 757.12926.493626.4578 -0.0149128 -4.77214 Coulomb-14 -199.523 14.949 14.158 -0.0519427 -16.6218 LJ (SR) -2670.5111.201109.688 0.1978463.3092 Coulomb (SR)739.79416.180715.4473 0.052135216.6834 pbc = xyz ;Run control integrator = md dt = 0.002 nsteps = 100 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype
