Re: [gmx-users] Reproducable MD runs on two PCs
I recompiled gromacs, lam, fftw3 on both PCs with the same version of intel compilers (before they were different, v. 10 12), set gen_vel=no and optimize_fft=no. With these changes I am getting agreement between two PCs within ~5% (was ~20% before). Ignore the nsteps value from the pasted mdp file. The actual run with ~20% difference was for the 30 ns run. I will test longer runs. Is there anything else to consider for better reproducability on two PCs? Hardware is the same, but OSes are RedHat and OpenSuse. On Sat, Nov 19, 2011 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/11/2011 10:10 PM, Igor Druz wrote: Hello, I am running MDs on a linux PC with OpenSuse, using: mpirun -np 4 mdrun -v -dlb auto -reprod If I repeat the calculation on the same PC, I get the same result. If I change to another PC with RedHat I get a different result. Yep. http://www.gromacs.org/Documentation/Terminology/Reproducibility More specifically, I am calculating a deviation from experiment, which varies by ~20 % on changing operating systems (pretty much the same hardware on both PCs). Is there any way to avoid such variations? I guess I am missing something in the mdp file, which is: Change your gen_vel seed and I bet you observe a similar variation on the same machine. There are rather few systems that will have equilibrated in 2ns, never mind converged. Mark cpp = /usr/bin/cpp -traditional integrator = sd tinit= 0 dt = 0.002 nsteps = 100 nstcomm = 1 nstcalcenergy= 1 nstxout = 5 nstvout = 100 nstlog = 100 nstenergy= 100 nstlist = 5 ns_type = grid pbc = xyz rlist= 0.9 optimize_fft = yes coulombtype = pme rcoulomb = 0.9 epsilon-r= 1 rvdw = 0.9 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-warnangle = 30 tc_grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = parrinello-rahman tau_p= 2 compressibility = 4.5e-05 ref_p= 1.0 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Many thanks for your help, Igor -- 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] Reproducable MD runs on two PCs
On 20/11/2011 7:31 PM, Igor Druz wrote: I recompiled gromacs, lam, fftw3 on both PCs with the same version of intel compilers (before they were different, v. 10 12), set gen_vel=no and optimize_fft=no. With these changes I am getting agreement between two PCs within ~5% (was ~20% before). Ignore the nsteps value from the pasted mdp file. The actual run with ~20% difference was for the 30 ns run. I will test longer runs. Is there anything else to consider for better reproducability on two PCs? Hardware is the same, but OSes are RedHat and OpenSuse. So far, you don't even know that the variation attributable to the difference in machines is significant compared to the intrinsic variation observed over replicates of the same kind of simulation on the same machine (e.g. different starting velocities). It's just not worth doing the work to study those effects... Mark On Sat, Nov 19, 2011 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 19/11/2011 10:10 PM, Igor Druz wrote: Hello, I am running MDs on a linux PC with OpenSuse, using: mpirun -np 4 mdrun -v -dlb auto -reprod If I repeat the calculation on the same PC, I get the same result. If I change to another PC with RedHat I get a different result. Yep. http://www.gromacs.org/Documentation/Terminology/Reproducibility More specifically, I am calculating a deviation from experiment, which varies by ~20 % on changing operating systems (pretty much the same hardware on both PCs). Is there any way to avoid such variations? I guess I am missing something in the mdp file, which is: Change your gen_vel seed and I bet you observe a similar variation on the same machine. There are rather few systems that will have equilibrated in 2ns, never mind converged. Mark cpp = /usr/bin/cpp -traditional integrator = sd tinit= 0 dt = 0.002 nsteps = 100 nstcomm = 1 nstcalcenergy= 1 nstxout = 5 nstvout = 100 nstlog = 100 nstenergy= 100 nstlist = 5 ns_type = grid pbc = xyz rlist= 0.9 optimize_fft = yes coulombtype = pme rcoulomb = 0.9 epsilon-r= 1 rvdw = 0.9 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-warnangle = 30 tc_grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = parrinello-rahman tau_p= 2 compressibility = 4.5e-05 ref_p= 1.0 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Many thanks for your help, Igor -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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] Problems with g_filter
Dear all I'm trying to use the follow command with a protein in DPPC and explicit water g_filter -s md.tpr -f md.xtc -ol movie_filtered.pdb -fit -nf 5 Altough I selected protein group, the command export everything (water + protein + dppc). How can I fix it? Thanks in advance-- 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] Reproducable MD runs on two PCs
If the -reprod option works fine and we can get complete reproducability on one machine, then I would think there must be a way of at least minimizing differences on two machines. I was hoping to pick on the experience with precision, whether it is worth having a go with a double precision compilation? Igor On Sun, Nov 20, 2011 at 9:16 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 20/11/2011 7:31 PM, Igor Druz wrote: I recompiled gromacs, lam, fftw3 on both PCs with the same version of intel compilers (before they were different, v. 10 12), set gen_vel=no and optimize_fft=no. With these changes I am getting agreement between two PCs within ~5% (was ~20% before). Ignore the nsteps value from the pasted mdp file. The actual run with ~20% difference was for the 30 ns run. I will test longer runs. Is there anything else to consider for better reproducability on two PCs? Hardware is the same, but OSes are RedHat and OpenSuse. So far, you don't even know that the variation attributable to the difference in machines is significant compared to the intrinsic variation observed over replicates of the same kind of simulation on the same machine (e.g. different starting velocities). It's just not worth doing the work to study those effects... Mark On Sat, Nov 19, 2011 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/11/2011 10:10 PM, Igor Druz wrote: Hello, I am running MDs on a linux PC with OpenSuse, using: mpirun -np 4 mdrun -v -dlb auto -reprod If I repeat the calculation on the same PC, I get the same result. If I change to another PC with RedHat I get a different result. Yep. http://www.gromacs.org/Documentation/Terminology/Reproducibility More specifically, I am calculating a deviation from experiment, which varies by ~20 % on changing operating systems (pretty much the same hardware on both PCs). Is there any way to avoid such variations? I guess I am missing something in the mdp file, which is: Change your gen_vel seed and I bet you observe a similar variation on the same machine. There are rather few systems that will have equilibrated in 2ns, never mind converged. Mark cpp = /usr/bin/cpp -traditional integrator = sd tinit= 0 dt = 0.002 nsteps = 100 nstcomm = 1 nstcalcenergy= 1 nstxout = 5 nstvout = 100 nstlog = 100 nstenergy= 100 nstlist = 5 ns_type = grid pbc = xyz rlist= 0.9 optimize_fft = yes coulombtype = pme rcoulomb = 0.9 epsilon-r= 1 rvdw = 0.9 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-warnangle = 30 tc_grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = parrinello-rahman tau_p= 2 compressibility = 4.5e-05 ref_p= 1.0 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Many thanks for your help, Igor -- 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 http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reproducable MD runs on two PCs
On 20/11/2011 9:11 PM, Igor Druz wrote: If the -reprod option works fine and we can get complete reproducability on one machine, then I would think there must be a way of at least minimizing differences on two machines. Sure. Make as many things as similar as you can. Just don't bother trying too hard. The first tiny difference sees the simulations diverge, and you likely cannot prevent such a difference occurring, even if the difference is just a different OS on identical hardware. Chaos is inescapable here. I was hoping to pick on the experience with precision, whether it is worth having a go with a double precision compilation? That will reduce the effect of differences that affect numerical accuracy but make things more than twice as slow. Mark Igor On Sun, Nov 20, 2011 at 9:16 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 20/11/2011 7:31 PM, Igor Druz wrote: I recompiled gromacs, lam, fftw3 on both PCs with the same version of intel compilers (before they were different, v. 10 12), set gen_vel=no and optimize_fft=no. With these changes I am getting agreement between two PCs within ~5% (was ~20% before). Ignore the nsteps value from the pasted mdp file. The actual run with ~20% difference was for the 30 ns run. I will test longer runs. Is there anything else to consider for better reproducability on two PCs? Hardware is the same, but OSes are RedHat and OpenSuse. So far, you don't even know that the variation attributable to the difference in machines is significant compared to the intrinsic variation observed over replicates of the same kind of simulation on the same machine (e.g. different starting velocities). It's just not worth doing the work to study those effects... Mark On Sat, Nov 19, 2011 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 19/11/2011 10:10 PM, Igor Druz wrote: Hello, I am running MDs on a linux PC with OpenSuse, using: mpirun -np 4 mdrun -v -dlb auto -reprod If I repeat the calculation on the same PC, I get the same result. If I change to another PC with RedHat I get a different result. Yep. http://www.gromacs.org/Documentation/Terminology/Reproducibility More specifically, I am calculating a deviation from experiment, which varies by ~20 % on changing operating systems (pretty much the same hardware on both PCs). Is there any way to avoid such variations? I guess I am missing something in the mdp file, which is: Change your gen_vel seed and I bet you observe a similar variation on the same machine. There are rather few systems that will have equilibrated in 2ns, never mind converged. Mark cpp = /usr/bin/cpp -traditional integrator = sd tinit= 0 dt = 0.002 nsteps = 100 nstcomm = 1 nstcalcenergy= 1 nstxout = 5 nstvout = 100 nstlog = 100 nstenergy= 100 nstlist = 5 ns_type = grid pbc = xyz rlist= 0.9 optimize_fft = yes coulombtype = pme rcoulomb = 0.9 epsilon-r= 1 rvdw = 0.9 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-warnangle = 30 tc_grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = parrinello-rahman tau_p= 2 compressibility = 4.5e-05 ref_p= 1.0 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Many thanks for your help, Igor -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org
Re: [gmx-users] g_wham error
rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained sufficiently at the desired distance. The error complains that bin 2 should have points at 0.366 nm, but it appears neither bin 1 nor bin 2 satisfy this requirement. Check carefully what you have set for reference distances and what distances were actually maintained during the sampling. You may need a stronger restraint or longer simulations. How long are the simulations? I see that you're starting the analysis on data after 2 ns, but how much does that leave? -Justin On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com wrote: Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a warning: WARNING, no data point in bin 2 (z=0.366256) ! You may not get a reasonable profile. Check your histograms! and my histogram contains a single peak. I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct this? With 15 windows, you should have 15 histograms. Plot with: xmgrace -nxy histo.xvg It will show you where the lack of sampling is. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_wham error
rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? From literature, I kept it at 3000. Those plots do look very strange. The PMF is almost a step function, which is certainly wrong. You may need either more simulation time or more frequent collection of data points, but at this stage I can only guess. Not much more I can offer, sorry. A stronger restraint would mean a stronger force constant, yes, but if you're using 3000 to restrain simple molecules like methane, I think there is no need to increase it. -Justin On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained sufficiently at the desired distance. The error complains that bin 2 should have points at 0.366 nm, but it appears neither bin 1 nor bin 2 satisfy this requirement. Check carefully what you have set for reference distances and what distances were actually maintained during the sampling. You may need a stronger restraint or longer simulations. How long are the simulations? I see that you're starting the analysis on data after 2 ns, but how much does that leave? -Justin On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com__ wrote: Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a warning: WARNING, no data point in bin 2 (z=0.366256) ! You may not get a reasonable profile. Check your histograms! and my histogram contains a single peak. I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct this? With 15 windows, you should have 15 histograms. Plot with: xmgrace -nxy histo.xvg It will show you where the lack of sampling is. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search 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] query on partial charge entry in topology
Hi, I find that in the ffnonbonded.itp under OPLS forcefield ( inside opls.ff directory), for each particle-type, there is a partial charge assigned to it. However, again in the .rtp file, for each residue, under each charge group, each of the atom is assigned another partial charge assigned to it. I wonder what are the purposes of having two partial charge entries and which charge is actually being used in simulation . My guess is that , the charge distribution assigned in the .rtp file is most probably the one being used during simulation. If so, then what is the purpose of having another partial charge entry in the ffnonbonded.itp. If someone can clarify the doubt, that will be great. Sanku-- 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] query on partial charge entry in topology
Sanku M wrote: Hi, I find that in the ffnonbonded.itp under OPLS forcefield ( inside opls.ff directory), for each particle-type, there is a partial charge assigned to it. However, again in the .rtp file, for each residue, under each charge group, each of the atom is assigned another partial charge assigned to it. I wonder what are the purposes of having two partial charge entries and which charge is actually being used in simulation . My guess is that , the charge distribution assigned in the .rtp file is most probably the one being used during simulation. If so, then what is the purpose of having another partial charge entry in the ffnonbonded.itp. If someone can clarify the doubt, that will be great. It is a relic of previous development in which charges could be generalized. The ones in the .rtp entries are used. Everything else is irrelevant. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS/ORCA QMMM
Dear Justin, The LJ and LJ.Excl files should be generated when you set bOpt = yes. What does the .inp file say. Is there !QMMMOpt or only !EnGrad? Christoph On 11/18/2011 06:20 PM, Jose Tusell wrote: Hi Justin, I tried using a larger step size but my system blew up... My guess is that I have a bad starting structure, I'll work on the initial structure for the QM region (energy minimize). When I'm running ORCA I want to have a LJ file to correct for the interaction of my QM system with the protein. However this file is not created when I run QMMM, I've used the bOpt = true in the mdp file. Can anyone please offer some help on how to create this LJ files? Thanks, Jose Tusell On Thu, Nov 17, 2011 at 2:07 PM, swati patelswatipatel...@gmail.com wrote: hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? Thanx with anticipation. On Fri, Nov 18, 2011 at 2:29 AM, Jose Tuselljrta1...@gmail.com wrote: I'll try changing the step size first and if that fails I'll try another algorithm. Thanks for the input. Jose Tusell On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkuljalem...@vt.edu wrote: Jose Tusell wrote: Hi Justin, Thanks for the input on why this is happening. It sounds a little suspicious that the energy doesn't change after a few steps of energy minimization. Do you know of any way that I can find out what is going on? The screen output should indicate the atom with maximal force. Sometimes the EM algorithms get stuck when the geometry cannot change without making detrimental moves. You either need a larger step size, a different algorithm, or a better starting structure, if that is the case. I have seen this many times before, nothing suspicious about it. -Justin Thanks, Jose Tusell On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkuljalem...@vt.edu wrote: Jose Tusell wrote: Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following: Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.21899e+041.92496e+035.62567e+031.49141e+01 3.68001e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41200e+041.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 11.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.20006e+041.92297e+035.62600e+031.47801e+01 3.67746e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41174e+041.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 22.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.17961e+041.92126e+035.62633e+031.46477e+01 3.67461e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41145e+041.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 33.00.0 Step Time Lambda 44.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 1.16705e+041.92041e+035.62652e+031.45728e+01 3.67282e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip.Quantum En. 2.41128e+041.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 55.00.0 Step Time Lambda 66.00.0 Step Time Lambda 77.00.0 Step Time Lambda 88.00.0 Step Time Lambda 99.00.0 Step Time Lambda 10 10.00.0 Step Time Lambda 11 11.00.0
[gmx-users] charmm 27 gromacs version mdp query
Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so I want to know your any suggestions and corrections in my mdp files (below), so that i can use the corrected mdp file to simulate the system. *1st mdp file :* title = Bilayer-500 cpp= /lib/cpp constraints= all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 200 ; 4 ns nstcomm= 1 nstxout= 5000 nstvout= 5000 nstfout= 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist= 10 ; long range interactions coulombtype= PME rlist = 1.2; neighborlist cut-off rcoulomb = 1.2; Coulomb cut-off rvdw = 1.2; VdW cut-off fourierspacing = 0.12; The maximum grid spacing for the FFT grid when using PPPM or PME pme_order = 4 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.01.0 compressibility= 4.5e-5 4.5e-5 ref_p = 1.01.0 gen_vel= yes gen_temp = 303.0 gen_seed = 478905 2nd mdp file: title = Bilayer-500 cpp= /lib/cpp constraints= all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 200 ; 4 ns nstcomm= 1 nstxout= 5000 nstvout= 5000 nstfout= 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist= 10 ; long range interactions rlist = 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.0 vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.01.0 compressibility= 4.5e-5 4.5e-5 ref_p = 1.01.0 gen_vel= yes gen_temp = 303.0 gen_seed = 478905 Your help is highly appreciated. Thanks Pramod -- 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] g_wham error
Justin, Should i turn off charges on the methane molecules? I have left them on. On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul jalem...@vt.edu wrote: rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? From literature, I kept it at 3000. Those plots do look very strange. The PMF is almost a step function, which is certainly wrong. You may need either more simulation time or more frequent collection of data points, but at this stage I can only guess. Not much more I can offer, sorry. A stronger restraint would mean a stronger force constant, yes, but if you're using 3000 to restrain simple molecules like methane, I think there is no need to increase it. -Justin On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained sufficiently at the desired distance. The error complains that bin 2 should have points at 0.366 nm, but it appears neither bin 1 nor bin 2 satisfy this requirement. Check carefully what you have set for reference distances and what distances were actually maintained during the sampling. You may need a stronger restraint or longer simulations. How long are the simulations? I see that you're starting the analysis on data after 2 ns, but how much does that leave? -Justin On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com**__ wrote: Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a warning: WARNING, no data point in bin 2 (z=0.366256) ! You may not get a reasonable profile. Check your histograms! and my histogram contains a single peak. I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct this? With 15 windows, you should have 15 histograms. Plot with: xmgrace -nxy histo.xvg It will show you where the lack of sampling is. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**__ vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**_ vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org ** http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users
Re: [gmx-users] g_wham error
rajat desikan wrote: Justin, Should i turn off charges on the methane molecules? I have left them on. What force field are you using? If you've got an all-atom model of methane, you should have partial charges. -Justin On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? From literature, I kept it at 3000. Those plots do look very strange. The PMF is almost a step function, which is certainly wrong. You may need either more simulation time or more frequent collection of data points, but at this stage I can only guess. Not much more I can offer, sorry. A stronger restraint would mean a stronger force constant, yes, but if you're using 3000 to restrain simple molecules like methane, I think there is no need to increase it. -Justin On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained sufficiently at the desired distance. The error complains that bin 2 should have points at 0.366 nm, but it appears neither bin 1 nor bin 2 satisfy this requirement. Check carefully what you have set for reference distances and what distances were actually maintained during the sampling. You may need a stronger restraint or longer simulations. How long are the simulations? I see that you're starting the analysis on data after 2 ns, but how much does that leave? -Justin On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com__ mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com wrote: Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a warning: WARNING, no data point in bin 2 (z=0.366256) ! You may not get a reasonable profile. Check your histograms! and my histogram contains a single peak. I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct this? With 15 windows, you should have 15 histograms. Plot with: xmgrace -nxy histo.xvg It will show you where the lack of sampling is. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu http://vt.edu | (540) 231-9080
Re: [gmx-users] g_wham error
Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple of doubts Justin. Since, I am pulling the methane away steadily, it should smoothly increase the distance right? But the second methane molecule is both increasing and decreasing it's position, sort of going back and forth. Also, one more thing. Originally, I had given the option for pull_dim as Y N N (x direction). But the second methane moved in all 3 directions. So I position restrained the second methane to the x axis (Fcx=0, Fcy=1000 and Fcz=1000)...does this have any bearing on my simulations? On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul jalem...@vt.edu wrote: rajat desikan wrote: Justin, Should i turn off charges on the methane molecules? I have left them on. What force field are you using? If you've got an all-atom model of methane, you should have partial charges. -Justin On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? From literature, I kept it at 3000. Those plots do look very strange. The PMF is almost a step function, which is certainly wrong. You may need either more simulation time or more frequent collection of data points, but at this stage I can only guess. Not much more I can offer, sorry. A stronger restraint would mean a stronger force constant, yes, but if you're using 3000 to restrain simple molecules like methane, I think there is no need to increase it. -Justin On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained sufficiently at the desired distance. The error complains that bin 2 should have points at 0.366 nm, but it appears neither bin 1 nor bin 2 satisfy this requirement. Check carefully what you have set for reference distances and what distances were actually maintained during the sampling. You may need a stronger restraint or longer simulations. How long are the simulations? I see that you're starting the analysis on data after 2 ns, but how much does that leave? -Justin On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** __ mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com** wrote: Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a warning: WARNING, no data point in bin 2 (z=0.366256) ! You may not get a reasonable profile. Check your histograms! and my histogram contains a single peak. I have pulled my other methane 1 nm away from the first methane. I have 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you please tell me how to correct this?
Re: [gmx-users] g_wham error
rajat desikan wrote: Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple This is fundamentally incorrect. 53A6 is a united-atom force field, so each methane should be a single particle with 0 charge using the CH4 atom type. of doubts Justin. Since, I am pulling the methane away steadily, it should smoothly increase the distance right? But the second methane molecule is both increasing and decreasing it's position, sort of going back and forth. This sounds like SMD, not umbrella sampling. Or are you referring to the pulling during which you generated configurations for umbrella sampling? Also, one more thing. Originally, I had given the option for pull_dim as Y N N (x direction). But the second methane moved in all 3 directions. There is no reason to suppose that pulling in only one dimension will necessarily be correct. The dissociation of two simple molecules can occur in 3 dimensions. So I position restrained the second methane to the x axis (Fcx=0, Fcy=1000 and Fcz=1000)...does this have any bearing on my simulations? It should be unnecessary to restrain either molecule. -Justin On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Justin, Should i turn off charges on the methane molecules? I have left them on. What force field are you using? If you've got an all-atom model of methane, you should have partial charges. -Justin On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? From literature, I kept it at 3000. Those plots do look very strange. The PMF is almost a step function, which is certainly wrong. You may need either more simulation time or more frequent collection of data points, but at this stage I can only guess. Not much more I can offer, sorry. A stronger restraint would mean a stronger force constant, yes, but if you're using 3000 to restrain simple molecules like methane, I think there is no need to increase it. -Justin On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained sufficiently at the desired distance. The error complains that bin 2 should have points at 0.366 nm, but it appears neither bin 1 nor bin 2 satisfy this requirement. Check carefully what you have set for reference distances and what distances were actually maintained during the sampling. You may need a stronger restraint or longer simulations. How long are the simulations? I see that you're starting the analysis on data after 2 ns, but how much does that leave? -Justin On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com__ mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com__ mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com mailto:rajatdesi...@gmail.com__ wrote: Oh lovely...thanks for the quick reply
Re: [gmx-users] g_wham error
rajat desikan wrote: Sorry, sorry...I have used Opls AA. The methane was going back and forth in the pulling during which I generated the configurations. Assuming you used a harmonic potential, that is to be expected. As long as you have set up reasonable spacing for your sampling windows from the snapshots along that trajectory, that should not be an issue. I also see no reason for uneven spacing in a system as simple as this one, though that's not a problem, per se, just not necessary. -Justin On Mon, Nov 21, 2011 at 3:28 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple This is fundamentally incorrect. 53A6 is a united-atom force field, so each methane should be a single particle with 0 charge using the CH4 atom type. of doubts Justin. Since, I am pulling the methane away steadily, it should smoothly increase the distance right? But the second methane molecule is both increasing and decreasing it's position, sort of going back and forth. This sounds like SMD, not umbrella sampling. Or are you referring to the pulling during which you generated configurations for umbrella sampling? Also, one more thing. Originally, I had given the option for pull_dim as Y N N (x direction). But the second methane moved in all 3 directions. There is no reason to suppose that pulling in only one dimension will necessarily be correct. The dissociation of two simple molecules can occur in 3 dimensions. So I position restrained the second methane to the x axis (Fcx=0, Fcy=1000 and Fcz=1000)...does this have any bearing on my simulations? It should be unnecessary to restrain either molecule. -Justin On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: Justin, Should i turn off charges on the methane molecules? I have left them on. What force field are you using? If you've got an all-atom model of methane, you should have partial charges. -Justin On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? From literature, I kept it at 3000. Those plots do look very strange. The PMF is almost a step function, which is certainly wrong. You may need either more simulation time or more frequent collection of data points, but at this stage I can only guess. Not much more I can offer, sorry. A stronger restraint would mean a stronger force constant, yes, but if you're using 3000 to restrain simple molecules like methane, I think there is no need to increase it. -Justin On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows
RE: [gmx-users] density
Last bit here, that is probably done using a RDF, which is a probability function, which you can then convert into a number of atoms in each shell. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Sunday, 20 November 2011 5:52 PM To: gmx-users@gromacs.org Subject: [gmx-users] density Dear Prof. I have problems about density. I equilibrated my system consist 500 surfactants and 6 water molecules in martini coarse-grained for 120 ns and my results of g_energy next pr.mdp for density are: average = 907.701 err.est = 0.61 rmsd = 2.54989 tot-drift = -3.4173 I don't know about good quantity of err.est, rmsd and tot-drift for density adjustment? and when my system has been equilibrated? May I know about my problem, please? On the other hand, density distribution for different groups of the system in terms of their distance from micell's COM distance is considered In the articles about surfactants. I think that it is possible with g_density but this program compute the density as the function of box(nm). May I know about this problem, Please? Best Regards sara -- 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] The time correlation functions for the orientation of the C-H
Check Chapter 8 and Appendix D of the manual. You can use g_analyze to generate an autocorrelation function for any data / property that you can feed it, if there isn't something built into a particular script. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of intra\sa175950 Sent: Friday, 18 November 2011 9:39 PM To: gmx-users@gromacs.org Subject: [gmx-users] The time correlation functions for the orientation of the C-H Hi GMX users, I am interesting to compute the tcf of C-H bonds for several surfactants in micelles. Is there a tool in GROMACS to do that ? Stephane -- 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] NVT simulation
If you are just getting a feel for these things, use the -v switch with mdrun, this makes it verbose, and prints out lots of messages letting you know how much longer it will be etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of swati patel Sent: Sunday, 20 November 2011 4:47 AM To: Discussion list for GROMACS users Subject: [gmx-users] NVT simulation hello Justin, I am running NVT simulation for 20,000 steps.From last 40 minutes,It is showing on the screen NOTE: Turning on dynamic load balancing and no further steps are shown.Do generally NVT simulation takes a good amount of time or am I making a mistake somwhere in the parameter file? Thanx -- 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] calculation equation of g_vanhove
Dear gmxers, I try to use g_vanhove in the gmx, but I do not find what it actually calculates because no equations are put in the manual. By the definition, it seems to be a bit different from those in some articles. Could you please give it clearly? Thanks a lot for any reply! Dr. Chaofu Wu -- Department of Chemistry and Materials Science Hunan University of Humanities, Science and Technology, Loudi 417000, the People's Republic of China (P.R. China)-- 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] GROMACS/ORCA QMMM
I've tried the bOpt = true. Is the flag bOpt = yes? I'll try that and I'll let you know. Ramon On Sun, Nov 20, 2011 at 1:19 PM, Christoph Riplinger c...@thch.uni-bonn.de wrote: Dear Justin, The LJ and LJ.Excl files should be generated when you set bOpt = yes. What does the .inp file say. Is there !QMMMOpt or only !EnGrad? Christoph On 11/18/2011 06:20 PM, Jose Tusell wrote: Hi Justin, I tried using a larger step size but my system blew up... My guess is that I have a bad starting structure, I'll work on the initial structure for the QM region (energy minimize). When I'm running ORCA I want to have a LJ file to correct for the interaction of my QM system with the protein. However this file is not created when I run QMMM, I've used the bOpt = true in the mdp file. Can anyone please offer some help on how to create this LJ files? Thanks, Jose Tusell On Thu, Nov 17, 2011 at 2:07 PM, swati patelswatipatel...@gmail.com wrote: hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? Thanx with anticipation. On Fri, Nov 18, 2011 at 2:29 AM, Jose Tuselljrta1...@gmail.com wrote: I'll try changing the step size first and if that fails I'll try another algorithm. Thanks for the input. Jose Tusell On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkuljalem...@vt.edu wrote: Jose Tusell wrote: Hi Justin, Thanks for the input on why this is happening. It sounds a little suspicious that the energy doesn't change after a few steps of energy minimization. Do you know of any way that I can find out what is going on? The screen output should indicate the atom with maximal force. Sometimes the EM algorithms get stuck when the geometry cannot change without making detrimental moves. You either need a larger step size, a different algorithm, or a better starting structure, if that is the case. I have seen this many times before, nothing suspicious about it. -Justin Thanks, Jose Tusell On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkuljalem...@vt.edu wrote: Jose Tusell wrote: Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following: Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.21899e+04 1.92496e+03 5.62567e+03 1.49141e+01 3.68001e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41200e+04 1.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 1 1.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.20006e+04 1.92297e+03 5.62600e+03 1.47801e+01 3.67746e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41174e+04 1.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 2 2.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.17961e+04 1.92126e+03 5.62633e+03 1.46477e+01 3.67461e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41145e+04 1.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 3 3.0 0.0 Step Time Lambda 4 4.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.16705e+04 1.92041e+03 5.62652e+03 1.45728e+01 3.67282e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41128e+04 1.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 5 5.0 0.0 Step Time Lambda 6 6.0 0.0 Step Time Lambda 7 7.0 0.0 Step Time Lambda 8 8.0 0.0 Step Time
Re: [gmx-users] GROMACS/ORCA QMMM
That solved it. In the ORCA manual for version 2.8 it says to use bOpt = true instead of bOpt = yes. And there is no mention of the mdp option in the gromacs manual or gromacs online mdp options. Ramon On Sun, Nov 20, 2011 at 4:57 PM, Jose Tusell jrta1...@gmail.com wrote: I've tried the bOpt = true. Is the flag bOpt = yes? I'll try that and I'll let you know. Ramon On Sun, Nov 20, 2011 at 1:19 PM, Christoph Riplinger c...@thch.uni-bonn.de wrote: Dear Justin, The LJ and LJ.Excl files should be generated when you set bOpt = yes. What does the .inp file say. Is there !QMMMOpt or only !EnGrad? Christoph On 11/18/2011 06:20 PM, Jose Tusell wrote: Hi Justin, I tried using a larger step size but my system blew up... My guess is that I have a bad starting structure, I'll work on the initial structure for the QM region (energy minimize). When I'm running ORCA I want to have a LJ file to correct for the interaction of my QM system with the protein. However this file is not created when I run QMMM, I've used the bOpt = true in the mdp file. Can anyone please offer some help on how to create this LJ files? Thanks, Jose Tusell On Thu, Nov 17, 2011 at 2:07 PM, swati patelswatipatel...@gmail.com wrote: hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? Thanx with anticipation. On Fri, Nov 18, 2011 at 2:29 AM, Jose Tuselljrta1...@gmail.com wrote: I'll try changing the step size first and if that fails I'll try another algorithm. Thanks for the input. Jose Tusell On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkuljalem...@vt.edu wrote: Jose Tusell wrote: Hi Justin, Thanks for the input on why this is happening. It sounds a little suspicious that the energy doesn't change after a few steps of energy minimization. Do you know of any way that I can find out what is going on? The screen output should indicate the atom with maximal force. Sometimes the EM algorithms get stuck when the geometry cannot change without making detrimental moves. You either need a larger step size, a different algorithm, or a better starting structure, if that is the case. I have seen this many times before, nothing suspicious about it. -Justin Thanks, Jose Tusell On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkuljalem...@vt.edu wrote: Jose Tusell wrote: Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following: Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.21899e+04 1.92496e+03 5.62567e+03 1.49141e+01 3.68001e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41200e+04 1.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 1 1.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.20006e+04 1.92297e+03 5.62600e+03 1.47801e+01 3.67746e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41174e+04 1.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 2 2.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.17961e+04 1.92126e+03 5.62633e+03 1.46477e+01 3.67461e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41145e+04 1.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 3 3.0 0.0 Step Time Lambda 4 4.0 0.0 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.16705e+04 1.92041e+03 5.62652e+03 1.45728e+01 3.67282e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41128e+04 1.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 5 5.0 0.0 Step
[gmx-users] charmm 27 FF mdp query
Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so I want to know your any suggestions and corrections in my mdp files (below), so that i can use the corrected mdp file to simulate the system. *1st mdp file :* title = Bilayer-500 cpp= /lib/cpp constraints= all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 200 ; 4 ns nstcomm= 1 nstxout= 5000 nstvout= 5000 nstfout= 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist= 10 ; long range interactions coulombtype= PME rlist = 1.2; neighborlist cut-off rcoulomb = 1.2; Coulomb cut-off rvdw = 1.2; VdW cut-off fourierspacing = 0.12; The maximum grid spacing for the FFT grid when using PPPM or PME pme_order = 4 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.01.0 compressibility= 4.5e-5 4.5e-5 ref_p = 1.01.0 gen_vel= yes gen_temp = 303.0 gen_seed = 478905 2nd mdp file: title = Bilayer-500 cpp= /lib/cpp constraints= all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 200 ; 4 ns nstcomm= 1 nstxout= 5000 nstvout= 5000 nstfout= 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist= 10 ; long range interactions rlist = 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.0 vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.01.0 compressibility= 4.5e-5 4.5e-5 ref_p = 1.01.0 gen_vel= yes gen_temp = 303.0 gen_seed = 478905 Your help is highly appreciated. Thanks Pramod -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about temperature coupling
Dear gmxusers. I have problems about temperature coupling. Here is my parameter for temperature coupling. ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 298 I used g_traj -f traj.xtc -s topol.tpr -ot temp.xvg to check the temperature for all time frames. The temperature of the system seems to fluctuate around 200K. My system consists 1000 waters and 18 NA and 18 CL. And the SOL alone has such problem. Could anyone give me a clue of what may be the cause of the misfit of the temperature? Thank you very much! Best Regards rtzhang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about temperature coupling
RuiTing Zhang wrote: Dear gmxusers. I have problems about temperature coupling. Here is my parameter for temperature coupling. ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 298 I used g_traj -f traj.xtc -s topol.tpr -ot temp.xvg to check the temperature for all time frames. The temperature of the system seems to fluctuate around 200K. My system consists 1000 waters and 18 NA and 18 CL. And the SOL alone has such problem. Could anyone give me a clue of what may be the cause of the misfit of the temperature? Thank you very much! Note that g_traj warns that constraints are not taken into consideration when printing temperatures. This is likely where the discrepancy lies. -Justin Best Regards rtzhang -- 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] about temperature coupling
On 21/11/2011 2:12 PM, RuiTing Zhang wrote: Dear gmxusers. I have problems about temperature coupling. Here is my parameter for temperature coupling. ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 298 I used g_traj -f traj.xtc -s topol.tpr -ot temp.xvg to check the temperature for all time frames. The temperature of the system seems to fluctuate around 200K. My system consists 1000 waters and 18 NA and 18 CL. And the SOL alone has such problem. Could anyone give me a clue of what may be the cause of the misfit of the temperature? Thank you very much! See g_traj -h. Your waters probably have constrained bonds. Use g_energy to observe the observations mdrun made about the temperature, if you chose a suitable value for nstenergy. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS/ORCA QMMM
When I run gromacs with bOpt yes I run into the a problem with the coordinates of my qm system: the initial coordinates are the following: NAME = ybu_em_qmmm.inp | 1 #input-file generated by gromacs | 2 !QMMMOpt TightSCF | 3 !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym | 4 %scf | 5 Maxiter 5000 | 6 end | 7 %pal nprocs 8 | 8 end | 9 | 10 | 11 | 12 %LJCOEFFICIENTS ybu_em_qmmm.LJ | 13 *xyz -2 1 | 14 7 46.448 40.2500010 48.1099987 | 15 6 45.2400017 40.2899981 47.564 | 16 7 44.7599983 40.6899977 46.3600016 | 17 6 43.4700012 40.594 46.055 | 18 7 42.631 40.1100016 46.9500017 | 19 6 43.0100012 39.674 48.161 | 20 7 42.1299982 39.146 49.015 | 21 1 42.433 38.814 49.9200010 | 22 1 41.1600018 39.082 48.7699986 | 23 6 44.342 39.770 48.490 | 24 7 45.070 39.4600010 49.5800018 | 25 6 46.3500023 39.767 49.344 | 26 6 47.765 40.530 47.497 | 27 8 48.811 41.0900021 48.3400011 | 28 6 49.8199987 41.710 47.4800014 | 29 6 47.7400017 41.5500021 46.3600016 | 30 8 46.981 41.448 45.1499987 | 31 1 47.235 40.594 44.674 | 32 6 49.1900015 41.911 46.113 | 33 8 49.7800016 40.8699989 45.332 | 34 1 50.7399988 41.0900021 45.1599979 | 35 6 50.070 43.2399988 47.570 | 36 8 51.445 43.5300016 47.9400015 | 37 15 51.842 43.3099985 49.475 | 38 8 52.104 44.805 49.9800014 | 39 8 50.5700016 42.500 50.064 | 40 8 53.1099987 42.3299980 49.3599987 | 41 15 54.473 43.1799984 49.4500017 | 42 8 55.5600023 42.1400023 48.884 | 43 8 54.1200018 44.475 48.555 | 44 8 54.537 43.5900021 50.990 | 45 15 55.8799982 43.354 51.844 | 46 8 57.0900011 43.9900017 50.988 | 47 8 55.8300018 43.9099979 53.223 | 48 8 56.1399984 41.7600012 51.844 | 49 1 43.1099987 40.921 45.123 | 50 1 47.168 39.639 50.0400019 | 51 1 48.1400013 39.6199989 47.0900011 | 52 1 47.3199987 42.4200010 46.8200016 | 53 1 49.339 42.896 45.717 | 54 1 50.723 41.1499977 47.4200010 | 55 1 49.866 43.689 46.6300011 | 56 1 49.4299984 43.6600018 48.3199978 | 57 12 51.387 43.3799982 51.9299984 | 58 * | 59 %pointcharges ybu_em_qmmm.pc | 60 | 61 | 62 END OF INPUT This first calculation doesn't run into problems however after this the new coordinates are wrong by a factor of 10. This is the next input file generated by gromacs: NAME = ybu_em_qmmm.inp | 1 #input-file generated by gromacs | 2 !QMMMOpt TightSCF | 3 !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym | 4 %scf | 5 Maxiter 5000 | 6 end | 7 %pal nprocs 8 | 8 end | 9 | 10 | 11 | 12 %LJCOEFFICIENTS ybu_em_qmmm.LJ | 13 *xyz -2 1 | 14 7 4.6643215 4.0067959 4.8652828 | 15 6 4.4694147 4.0687612 4.6910113 | 16 7 4.4788954 4.0736303 4.5814043 | 17 6 4.2882785 4.0960234 4.5192298 | 18 7 4.1568694 3.9851558 4.6636197 | 19 6 4.2702511 3.9942223 4.8413402 | 20 7 4.1388491 3.8647231 4.9325246 | 21 1 4.2422304 3.8729668 5.0225985 | 22 1 4.0874949 3.9029175 4.8758829 | 23 6 4.4479644 3.9264068 4.8907641 | 24 7 4.4724247 3.8935867 5.0617158 | 25 6 4.6581322 3.9623603 4.9860328 | 26 6 4.7224784 3.9516553 4.7729388 | 27 8 4.9013394 4.1037330 4.9433815 | 28 6 5.0506485 4.1505158 4.7845429 | 29 6 4.7479546 4.2596489 4.5867884 | 30 8 4.6396983 4.1753584 4.3912268 | 31 1 4.7245148 4.0333679 4.4395000 | 32 6 4.9467531 4.1628179 4.5303190 | 33 8 5.0127959 4.0332937 4.4357231 | 34 1 5.0972128 4.1086709 4.5025694 | 35 6 4.9707726 4.4155064 4.7358957 | 36 8 5.1747119 4.3822494 4.7240046 | 37 15 5.1759595 4.3526104 4.9696961 | 38 8 5.2000558 4.5951414 5.0385225 | 39 8 4.9872991 4.2056358 5.0856835 | 40 8 5.3196424 4.1316289 4.9306369 | 41 15 5.4781163 4.3365851 4.9144840 | 42 8 5.6436682 4.1501650 4.8309124 | 43 8 5.4556131 4.5460758 4.7758737 | 44 8 5.4388809 4.3959689 5.1872373 | 45 15 5.6339312 4.3419433 5.2184927 | 46 8 5.8053279 4.4479111 5.0789297 | 47 8 5.5981785 4.4297397 5.4245871 | 48 8 5.6559128 4.0851763 5.2241915 | 49 1 4.2944524 4.1013804 4.4863331 | 50 1 4.7380015 3.9515409 5.0357658 | 51 1 4.8261809 3.9258796 4.7002071 | 52 1 4.7115117 4.2592505 4.6899751 | 53 1 4.9388400 4.3221569 4.5484522 | 54 1 5.1027077 4.0887082 4.7342393 | 55 1 4.9870053 4.3987840 4.6446544 | 56 1 4.9254298 4.3886098 4.8489299 | 57 12 5.1316565 4.3423077 5.2266484 | 58 * | 59 %pointcharges ybu_em_qmmm.pc | 60 | 61 | 62 END OF INPUT Any ideas why this is happening?
[gmx-users] Increasing time for simulation
Dear Justin, I am very sorry for a very basic question as i am beginner in Gromacs. Kindly do tell me that how can I increase time for the simulation. like 1st time i ran experiment on 1ns now i want to increase the time. kindly tell me that how can I do it and also tell that for a protein complex simulation, how much time would be enough to study the system in a good way as you told that 1ns is very short to study such type of system. many thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] GROMACS/ORCA QMMM
Jose Tusell wrote: When I run gromacs with bOpt yes I run into the a problem with the coordinates of my qm system: the initial coordinates are the following: NAME = ybu_em_qmmm.inp | 1 #input-file generated by gromacs | 2 !QMMMOpt TightSCF | 3 !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym | 4 %scf | 5 Maxiter 5000 | 6 end | 7 %pal nprocs 8 | 8 end | 9 | 10 | 11 | 12 %LJCOEFFICIENTS ybu_em_qmmm.LJ | 13 *xyz -2 1 | 14 7 46.448 40.2500010 48.1099987 | 15 6 45.2400017 40.2899981 47.564 | 16 7 44.7599983 40.6899977 46.3600016 | 17 6 43.4700012 40.594 46.055 | 18 7 42.631 40.1100016 46.9500017 | 19 6 43.0100012 39.674 48.161 | 20 7 42.1299982 39.146 49.015 | 21 1 42.433 38.814 49.9200010 | 22 1 41.1600018 39.082 48.7699986 | 23 6 44.342 39.770 48.490 | 24 7 45.070 39.4600010 49.5800018 | 25 6 46.3500023 39.767 49.344 | 26 6 47.765 40.530 47.497 | 27 8 48.811 41.0900021 48.3400011 | 28 6 49.8199987 41.710 47.4800014 | 29 6 47.7400017 41.5500021 46.3600016 | 30 8 46.981 41.448 45.1499987 | 31 1 47.235 40.594 44.674 | 32 6 49.1900015 41.911 46.113 | 33 8 49.7800016 40.8699989 45.332 | 34 1 50.7399988 41.0900021 45.1599979 | 35 6 50.070 43.2399988 47.570 | 36 8 51.445 43.5300016 47.9400015 | 37 15 51.842 43.3099985 49.475 | 38 8 52.104 44.805 49.9800014 | 39 8 50.5700016 42.500 50.064 | 40 8 53.1099987 42.3299980 49.3599987 | 41 15 54.473 43.1799984 49.4500017 | 42 8 55.5600023 42.1400023 48.884 | 43 8 54.1200018 44.475 48.555 | 44 8 54.537 43.5900021 50.990 | 45 15 55.8799982 43.354 51.844 | 46 8 57.0900011 43.9900017 50.988 | 47 8 55.8300018 43.9099979 53.223 | 48 8 56.1399984 41.7600012 51.844 | 49 1 43.1099987 40.921 45.123 | 50 1 47.168 39.639 50.0400019 | 51 1 48.1400013 39.6199989 47.0900011 | 52 1 47.3199987 42.4200010 46.8200016 | 53 1 49.339 42.896 45.717 | 54 1 50.723 41.1499977 47.4200010 | 55 1 49.866 43.689 46.6300011 | 56 1 49.4299984 43.6600018 48.3199978 | 57 12 51.387 43.3799982 51.9299984 | 58 * | 59 %pointcharges ybu_em_qmmm.pc | 60 | 61 | 62 END OF INPUT This first calculation doesn't run into problems however after this the new coordinates are wrong by a factor of 10. This is the next input file generated by gromacs: NAME = ybu_em_qmmm.inp | 1 #input-file generated by gromacs | 2 !QMMMOpt TightSCF | 3 !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym | 4 %scf | 5 Maxiter 5000 | 6 end | 7 %pal nprocs 8 | 8 end | 9 | 10 | 11 | 12 %LJCOEFFICIENTS ybu_em_qmmm.LJ | 13 *xyz -2 1 | 14 7 4.6643215 4.0067959 4.8652828 | 15 6 4.4694147 4.0687612 4.6910113 | 16 7 4.4788954 4.0736303 4.5814043 | 17 6 4.2882785 4.0960234 4.5192298 | 18 7 4.1568694 3.9851558 4.6636197 | 19 6 4.2702511 3.9942223 4.8413402 | 20 7 4.1388491 3.8647231 4.9325246 | 21 1 4.2422304 3.8729668 5.0225985 | 22 1 4.0874949 3.9029175 4.8758829 | 23 6 4.4479644 3.9264068 4.8907641 | 24 7 4.4724247 3.8935867 5.0617158 | 25 6 4.6581322 3.9623603 4.9860328 | 26 6 4.7224784 3.9516553 4.7729388 | 27 8 4.9013394 4.1037330 4.9433815 | 28 6 5.0506485 4.1505158 4.7845429 | 29 6 4.7479546 4.2596489 4.5867884 | 30 8 4.6396983 4.1753584 4.3912268 | 31 1 4.7245148 4.0333679 4.4395000 | 32 6 4.9467531 4.1628179 4.5303190 | 33 8 5.0127959 4.0332937 4.4357231 | 34 1 5.0972128 4.1086709 4.5025694 | 35 6 4.9707726 4.4155064 4.7358957 | 36 8 5.1747119 4.3822494 4.7240046 | 37 15 5.1759595 4.3526104 4.9696961 | 38 8 5.2000558 4.5951414 5.0385225 | 39 8 4.9872991 4.2056358 5.0856835 | 40 8 5.3196424 4.1316289 4.9306369 | 41 15 5.4781163 4.3365851 4.9144840 | 42 8 5.6436682 4.1501650 4.8309124 | 43 8 5.4556131 4.5460758 4.7758737 | 44 8 5.4388809 4.3959689 5.1872373 | 45 15 5.6339312 4.3419433 5.2184927 | 46 8 5.8053279 4.4479111 5.0789297 | 47 8 5.5981785 4.4297397 5.4245871 | 48 8 5.6559128 4.0851763 5.2241915 | 49 1 4.2944524 4.1013804 4.4863331 | 50 1 4.7380015 3.9515409 5.0357658 | 51 1 4.8261809 3.9258796 4.7002071 | 52 1 4.7115117 4.2592505 4.6899751 | 53 1 4.9388400 4.3221569 4.5484522 | 54 1 5.1027077 4.0887082 4.7342393 | 55 1 4.9870053 4.3987840 4.6446544 | 56 1 4.9254298 4.3886098 4.8489299 | 57 12 5.1316565 4.3423077 5.2266484 | 58 * | 59 %pointcharges ybu_em_qmmm.pc | 60 | 61 | 62 END OF INPUT Any ideas why
Re: [gmx-users] GROMACS/ORCA QMMM
Yes. But where does the code go wrong? I'm reading the qm_orca.c file but I can't seem to know exactly were the factor of 10 is not accounted for. I see the factor of ten when going from gromacs to orca in (lines 219 to 221 of qm_orca.c file): qm-xQM[i][XX]/0.1, qm-xQM[i][YY]/0.1, qm-xQM[i][ZZ]/0.1); I just don't know where to look for the factor of 10 in the code. Could anyone point me to this? Thanks, Jose Tusell On Sun, Nov 20, 2011 at 10:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jose Tusell wrote: When I run gromacs with bOpt yes I run into the a problem with the coordinates of my qm system: the initial coordinates are the following: NAME = ybu_em_qmmm.inp | 1 #input-file generated by gromacs | 2 !QMMMOpt TightSCF | 3 !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym | 4 %scf | 5 Maxiter 5000 | 6 end | 7 %pal nprocs 8 | 8 end | 9 | 10 | 11 | 12 %LJCOEFFICIENTS ybu_em_qmmm.LJ | 13 *xyz -2 1 | 14 7 46.448 40.2500010 48.1099987 | 15 6 45.2400017 40.2899981 47.564 | 16 7 44.7599983 40.6899977 46.3600016 | 17 6 43.4700012 40.594 46.055 | 18 7 42.631 40.1100016 46.9500017 | 19 6 43.0100012 39.674 48.161 | 20 7 42.1299982 39.146 49.015 | 21 1 42.433 38.814 49.9200010 | 22 1 41.1600018 39.082 48.7699986 | 23 6 44.342 39.770 48.490 | 24 7 45.070 39.4600010 49.5800018 | 25 6 46.3500023 39.767 49.344 | 26 6 47.765 40.530 47.497 | 27 8 48.811 41.0900021 48.3400011 | 28 6 49.8199987 41.710 47.4800014 | 29 6 47.7400017 41.5500021 46.3600016 | 30 8 46.981 41.448 45.1499987 | 31 1 47.235 40.594 44.674 | 32 6 49.1900015 41.911 46.113 | 33 8 49.7800016 40.8699989 45.332 | 34 1 50.7399988 41.0900021 45.1599979 | 35 6 50.070 43.2399988 47.570 | 36 8 51.445 43.5300016 47.9400015 | 37 15 51.842 43.3099985 49.475 | 38 8 52.104 44.805 49.9800014 | 39 8 50.5700016 42.500 50.064 | 40 8 53.1099987 42.3299980 49.3599987 | 41 15 54.473 43.1799984 49.4500017 | 42 8 55.5600023 42.1400023 48.884 | 43 8 54.1200018 44.475 48.555 | 44 8 54.537 43.5900021 50.990 | 45 15 55.8799982 43.354 51.844 | 46 8 57.0900011 43.9900017 50.988 | 47 8 55.8300018 43.9099979 53.223 | 48 8 56.1399984 41.7600012 51.844 | 49 1 43.1099987 40.921 45.123 | 50 1 47.168 39.639 50.0400019 | 51 1 48.1400013 39.6199989 47.0900011 | 52 1 47.3199987 42.4200010 46.8200016 | 53 1 49.339 42.896 45.717 | 54 1 50.723 41.1499977 47.4200010 | 55 1 49.866 43.689 46.6300011 | 56 1 49.4299984 43.6600018 48.3199978 | 57 12 51.387 43.3799982 51.9299984 | 58 * | 59 %pointcharges ybu_em_qmmm.pc | 60 | 61 | 62 END OF INPUT This first calculation doesn't run into problems however after this the new coordinates are wrong by a factor of 10. This is the next input file generated by gromacs: NAME = ybu_em_qmmm.inp | 1 #input-file generated by gromacs | 2 !QMMMOpt TightSCF | 3 !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym | 4 %scf | 5 Maxiter 5000 | 6 end | 7 %pal nprocs 8 | 8 end | 9 | 10 | 11 | 12 %LJCOEFFICIENTS ybu_em_qmmm.LJ | 13 *xyz -2 1 | 14 7 4.6643215 4.0067959 4.8652828 | 15 6 4.4694147 4.0687612 4.6910113 | 16 7 4.4788954 4.0736303 4.5814043 | 17 6 4.2882785 4.0960234 4.5192298 | 18 7 4.1568694 3.9851558 4.6636197 | 19 6 4.2702511 3.9942223 4.8413402 | 20 7 4.1388491 3.8647231 4.9325246 | 21 1 4.2422304 3.8729668 5.0225985 | 22 1 4.0874949 3.9029175 4.8758829 | 23 6 4.4479644 3.9264068 4.8907641 | 24 7 4.4724247 3.8935867 5.0617158 | 25 6 4.6581322 3.9623603 4.9860328 | 26 6 4.7224784 3.9516553 4.7729388 | 27 8 4.9013394 4.1037330 4.9433815 | 28 6 5.0506485 4.1505158 4.7845429 | 29 6 4.7479546 4.2596489 4.5867884 | 30 8 4.6396983 4.1753584 4.3912268 | 31 1 4.7245148 4.0333679 4.4395000 | 32 6 4.9467531 4.1628179 4.5303190 | 33 8 5.0127959 4.0332937 4.4357231 | 34 1 5.0972128 4.1086709 4.5025694 | 35 6 4.9707726 4.4155064 4.7358957 | 36 8 5.1747119 4.3822494 4.7240046 | 37 15 5.1759595 4.3526104 4.9696961 | 38 8 5.2000558 4.5951414 5.0385225 | 39 8 4.9872991 4.2056358 5.0856835 | 40 8 5.3196424 4.1316289 4.9306369 | 41 15 5.4781163 4.3365851 4.9144840 | 42 8 5.6436682 4.1501650 4.8309124 | 43 8 5.4556131 4.5460758 4.7758737 | 44 8 5.4388809 4.3959689 5.1872373 | 45 15 5.6339312 4.3419433 5.2184927 | 46 8
Re: [gmx-users] Increasing time for simulation
Saba Ferdous wrote: Dear Justin, I am very sorry for a very basic question as i am beginner in Gromacs. Kindly do tell me that how can I increase time for the simulation. like 1st time i ran experiment on 1ns now i want to increase the time. kindly tell me that how can I do it and also tell that for a protein complex simulation, how much time would be enough to study the system in a good way as you told that 1ns is very short to study such type of system. The required time depends on the question being asked. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about temperature coupling
Dear Justin and Mark： Thank you for your kind help！I think I figure out the problem Best Regards rtzhang -- 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
