Re: [gmx-users] REMD slow's down drastically
Goods to know, thanks. Mileage certainly does vary. Mark On Feb 25, 2014 3:45 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Thank you Mark for the tips about the pinoffset. I'll try it and see if it affects the speed at all. Regarding the utility of hyperthreading, running on a cluster in which each node has 8 Nehalem processing cores, I have seen 5-15% speedup from using hyperthreading via 16 threads vs. using only 8 threads (in non-MPI gromacs). This is across about 10 simulations systems that I have worked on in the last four years. In all these cases, I am using -npme 0. However, once multiple nodes and IB fabric get involved, then hyperthreading gives no benefit and generally degrades the performance. Perhaps there are some other things getting involved here, but the only change I make is mdrun -nt 8 or mdrun -nt 16 and I see a speedup from -nt 16. System sizes range from 10K to 250K atoms. Note that I have never tried using the hyperthreading with REMD or any other fancy setup. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham mark.j.abra...@gmail.com Sent: 24 February 2014 21:26 To: Discussion list for GROMACS users Subject: Re: [gmx-users] REMD slow's down drastically On Feb 24, 2014 11:01 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Presuming that you have indeed set up the number of processors correctly (should be running on a different number of cored for different number of replicas to do a fair test), could it be a thread pinning issue? Yes, but part of the larger problem of over-loading the physical cores. I run on a Nehalem system with 8 cores/node but, because of the Nehalem hyperthreading (I think), gromacs always complains if I run mpirun -np $N mdrun where $N is the number of cores NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). However, if I use $N = 2 times the number of cores, then I don't get that note, instead getting: Pinning threads with a logical core stride of 1 Aside, if anybody has a suggestion about how I should handle the thread pinning in my case, or if it matters, then I would be happy to hear it (my throughput seems to be good though). Hyper-threading is good for applications that are memory- or user-bound (so enabled by default on consumer machines), so they can take advantage of CPU instruction-issue opportunities while stalled. GROMACS kernels are already CPU-bound, so there is little to gain and it generally does not pay for the overhead. Generally, one should not use HT; turning it off can be emulated with the right use of -pinoffset and using half the number of threads. Finally, this comment is off topic, but you might want to reconsider having the CL ions in a separate temperature coupling group. Indeed. Mark Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Singam Karthick sikar...@yahoo.in Sent: 24 February 2014 02:32 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] REMD slow's down drastically Dear members, I am trying to run REMD simulation for poly Alanine (12 residue) system. I used remd generator to get the range of temperature with the exchange probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its drastically slow down the simulation time (for 70 pico seconds it took around 17 hours ) could anyone please tell me how to solve this issue. Following is the MDP file title = G4Ga3a4a5 production. ;define = ;-DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 1250 ; 2 * 500 = 3ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 0.2 ps nstvout = 1 ; save velocities every 0.2 ps nstxtcout = 500 ; save xtc coordinate every 0.2 ps nstenergy = 500 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = hbonds; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy morse = no ; Neighborsearching ns_type = grid ; search
[gmx-users] (Implicit Solvation) Effect of van der waal radii on dynamics of ion
I am trying to run a simulation of single Na ion in implicit solvent(water), with OPLSAA FF in gromacs 4.5.7. In particular I want to find the effect of the gbr parameter in the gbsa.itp file in /gromacs-4.5.7d/share/gromacs/top/oplsaa.ff. [ implicit_genborn_params ] ; atypesarstpi gbrhct opls_102 0.16 1 1.2150.1625 0.79 ; N (RNH3+) opls_135 0.2 1 0.8800.1900.72 ; CB opls_136 0.19 1 1.0450.1900.72 ; CB I tried to run a simulation with three different values for the gbr parameter. After the mdrun I find that the trajectory remains the same for all three cases. So what exactly is the effect of this parameter on the dynamics in implicit solvent method? Or am I missing something? Any help is much appreciated. Nichith - .mdp file : integrator = sd nsteps = 100 dt = 0.002 implicit_solvent = GBSA gb_algorithm = Still gb_epsilon_solvent = 80 comm_mode = none pbc= no nstlist = 0 ns_type = simple rlist= 0 rgbradii = 0 coulombtype= Cut-off rcoulomb = 0 vdwtype = Cut-off rvdw = 0 tcoupl = v-rescale tc_grps = system tau_t = 0.1 ref_t = 300 ;energygrps = Ion_chain_A Ion_chain_B gen_vel = yes gen_temp = 300 ld_seed = 10092 gen_seed = 10092 nstxout = 100 nstvout = 100 nstxtcout= 100 nstenergy= 100 -- View this message in context: http://gromacs.5086.x6.nabble.com/Implicit-Solvation-Effect-of-van-der-waal-radii-on-dynamics-of-ion-tp5014788.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dubious results with NPT
your average pressure is the pressure you should report in the publication. if you got 5 bars instead of 1 bar, you should write I simulated the system at 5 bars Dr. Vitaly V. Chaban On Tue, Feb 25, 2014 at 6:01 AM, sujithkakkat . sujithk...@gmail.com wrote: On Mon, Feb 24, 2014 at 5:37 AM, sujithkakkat . sujithk...@gmail.com wrote: Hello, Thank you both for the comments. I am using gromos96 forcefield . I read a little bit and as you said the nonbonded cutoff has to be higher. The tau_p=5ps was chosen , since the manual mentions that the value has to be raised by 4-5 times on going from berendsen to parrinello-rahman barostat, though I did not completely follow the reasons behind it. I will try with lower values. I had run an earlier simulation with the same parameters for a pure water system for 5ns and reference pressure 5bar, and things worked fine there with the average pressure at 5.15bar. No, this average pressure is not fine. Why isn't it fine? I admit it is not very good. I guess due to huge fluctuations the average pressure is tend to vary a bit to either side of the reference value, unless I continue the equilibration for a very long time. Also the average was calculated with g_energy, which I guess considered the entire simulation, where the first few time steps, when the system is away from equilibrium, would have poor pressure values with respect to reference , which would reflect in the average pressure calculated. Also using g_analyze to calculate average pressure between different times during the simulation did not give the same value. So I am not sure if I should aim at an average pressure which is equal to the reference pressure. Thanks, Sujith. On Mon, Feb 24, 2014 at 4:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/23/14, 11:37 PM, sujithkakkat . wrote: Hello, Thank you both for the comments. I am using gromos96 forcefield . I read a little bit and as you said the nonbonded cutoff has to be higher. The tau_p=5ps was chosen , since the manual mentions that the value has to be raised by 4-5 times on going from berendsen to parrinello-rahman barostat, though I did not completely follow the reasons behind it. I will try with lower values. I had run an earlier simulation with the same parameters for a pure water system for 5ns and reference pressure 5bar, and things worked fine there with the average pressure at 5.15bar. I guess the sigma for the case of water was low and therefore the small cut-off of 0.8nm did not matter. However the case of cyclohexane alone remains to be tried. I guess Dr Vitaly was saying about using a switch/shift function. I will try the simulation with the new settings and see. The Gromos force fields were parametrized with a plain cutoff for van der Waals. They do not require switching or shifting. It's true that plain cutoffs are a bit harsh, but switching and shifting have their own issues, and one should always stick to the parametrization methods unless there is demonstrable evidence that the new method is better. I have never known Gromos96 force fields to need anything other than plain cutoff for van der Waals to function as expected. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Binning of Free Energy landscapes
Hi, I was wondering as to what exactly happens during the binning of Free Energy Landscapes as generated by g_sham? I generated Free Energy Landscapes using g_sham and my Principal Components but I am trying to understand what does bin account for and how exactly does it function? Kind regards -- Ankita Naithani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (Implicit Solvation) Effect of van der waal radii on dynamics of ion
On Tue, Feb 25, 2014 at 9:41 AM, nichith nich...@gmail.com wrote: I am trying to run a simulation of single Na ion in implicit solvent(water), with OPLSAA FF in gromacs 4.5.7. In particular I want to find the effect of the gbr parameter in the gbsa.itp file in /gromacs-4.5.7d/share/gromacs/top/oplsaa.ff. [ implicit_genborn_params ] ; atypesarstpi gbrhct opls_102 0.16 1 1.2150.1625 0.79 ; N (RNH3+) opls_135 0.2 1 0.8800.1900.72 ; CB opls_136 0.19 1 1.0450.1900.72 ; CB I tried to run a simulation with three different values for the gbr parameter. After the mdrun I find that the trajectory remains the same for all three cases. So what exactly is the effect of this parameter on the dynamics in implicit solvent method? Or am I missing something? With a single ion, the only thing you can observe is the energy, right? Does that differ? If not, then there's a problem. You may not be sourcing the correct .itp file when you re-run grompp (e.g. check by making a deliberate syntax error). Or there may be a code problem (don't think this was a fix any time, but you could try with 4.6.5). Any help is much appreciated. Nichith - .mdp file : integrator = sd nsteps = 100 dt = 0.002 implicit_solvent = GBSA gb_algorithm = Still gb_epsilon_solvent = 80 comm_mode = none As grompp should be warning you, this is generally not good practice in these kinds of simulations. Angular is better, IIRC. Here, all you are probably observing in the trajectory is the propagation of the velocity, since there can be no force. Mark pbc= no nstlist = 0 ns_type = simple rlist= 0 rgbradii = 0 coulombtype= Cut-off rcoulomb = 0 vdwtype = Cut-off rvdw = 0 tcoupl = v-rescale tc_grps = system tau_t = 0.1 ref_t = 300 ;energygrps = Ion_chain_A Ion_chain_B gen_vel = yes gen_temp = 300 ld_seed = 10092 gen_seed = 10092 nstxout = 100 nstvout = 100 nstxtcout= 100 nstenergy= 100 -- View this message in context: http://gromacs.5086.x6.nabble.com/Implicit-Solvation-Effect-of-van-der-waal-radii-on-dynamics-of-ion-tp5014788.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Combine parts
Dear Gmx-user; How can I combine parts of my simulation after final MD? The results of my MD are splitted to several parts with .tgz format. Best Regards Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Combine parts
On Tue, Feb 25, 2014 at 4:45 PM, Hassan Aaryapour hassan.grom...@gmail.comwrote: Dear Gmx-user; How can I combine parts of my simulation after final MD? The results of my MD are splitted to several parts with .tgz format. Dear Hassan, Gromacs trajectories are written in .trr or .xtc format. These trajectories can be combined with trjcat command (see trjcat -h). .tgz is a compressed file. Presumably, Gromacs has nothing to do with this. Chandan -- Chandan Kumar Choudhury NCL, Pune INDIA Best Regards Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dubious results with NPT
No full solutions to this problem -- I'll write a few notes. * With large systems run for relatively small amounts of time, the ensemble could be statistically indistinguishble from the true distribution even if the averages don't line up correctly. See: http://pubs.acs.org/doi/abs/10.1021/ct300688p For ways to examine the full distribution of volumes. * Parrinello-Rahman isn't quite correct in GROMACS because virial and kinetic energy are offset by 1/2 a step, though getting something more like 1.2 atm when running at 1 atm is more common. * Note that with systems that are heterogeneous in direction (not uniform in x y and z), any errors in the pressure may be magnified. * If you have a property that changes when the pressure changes from 1 to 5 atm, odds are that molecular simulation is not the right way to study it -- the force fields are not that accurate. On Tue, Feb 25, 2014 at 6:48 AM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: in that case the average is reasonable, but you should state in the manuscript that all the reported results correspond to 5.15 bar. Dr. Vitaly V. Chaban On Tue, Feb 25, 2014 at 10:42 AM, sujithkakkat . sujithk...@gmail.com wrote: Hi, In fact the average pressure 5.15 bar was obtained for the case where the reference pressure was 5 bar. I had mentioned it in one of the previous mails. But still the average value is not that good. I had run an earlier simulation with the same parameters for a pure water system for 5ns and reference pressure 5bar, and things worked fine there with the average pressure at 5.15bar. Sujith. On Tue, Feb 25, 2014 at 2:29 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: your average pressure is the pressure you should report in the publication. if you got 5 bars instead of 1 bar, you should write I simulated the system at 5 bars Dr. Vitaly V. Chaban On Tue, Feb 25, 2014 at 6:01 AM, sujithkakkat . sujithk...@gmail.com wrote: On Mon, Feb 24, 2014 at 5:37 AM, sujithkakkat . sujithk...@gmail.com wrote: Hello, Thank you both for the comments. I am using gromos96 forcefield . I read a little bit and as you said the nonbonded cutoff has to be higher. The tau_p=5ps was chosen , since the manual mentions that the value has to be raised by 4-5 times on going from berendsen to parrinello-rahman barostat, though I did not completely follow the reasons behind it. I will try with lower values. I had run an earlier simulation with the same parameters for a pure water system for 5ns and reference pressure 5bar, and things worked fine there with the average pressure at 5.15bar. No, this average pressure is not fine. Why isn't it fine? I admit it is not very good. I guess due to huge fluctuations the average pressure is tend to vary a bit to either side of the reference value, unless I continue the equilibration for a very long time. Also the average was calculated with g_energy, which I guess considered the entire simulation, where the first few time steps, when the system is away from equilibrium, would have poor pressure values with respect to reference , which would reflect in the average pressure calculated. Also using g_analyze to calculate average pressure between different times during the simulation did not give the same value. So I am not sure if I should aim at an average pressure which is equal to the reference pressure. Thanks, Sujith. On Mon, Feb 24, 2014 at 4:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/23/14, 11:37 PM, sujithkakkat . wrote: Hello, Thank you both for the comments. I am using gromos96 forcefield . I read a little bit and as you said the nonbonded cutoff has to be higher. The tau_p=5ps was chosen , since the manual mentions that the value has to be raised by 4-5 times on going from berendsen to parrinello-rahman barostat, though I did not completely follow the reasons behind it. I will try with lower values. I had run an earlier simulation with the same parameters for a pure water system for 5ns and reference pressure 5bar, and things worked fine there with the average pressure at 5.15bar. I guess the sigma for the case of water was low and therefore the small cut-off of 0.8nm did not matter. However the case of cyclohexane alone remains to be tried. I guess Dr Vitaly was saying about using a switch/shift function. I will try the simulation with the new settings and see. The Gromos force fields were parametrized with a plain cutoff for van der Waals. They do not require switching or shifting. It's true that plain cutoffs are a bit harsh, but switching and shifting have their own issues, and one should always stick to the parametrization methods unless there is demonstrable evidence that the new method is better. I have never known Gromos96 force fields to need anything other than
Re: [gmx-users] Dubious results with NPT
On Tue, Feb 25, 2014 at 3:57 PM, Michael Shirts mrshi...@gmail.com wrote: No full solutions to this problem -- I'll write a few notes. * With large systems run for relatively small amounts of time, the ensemble could be statistically indistinguishble from the true distribution even if the averages don't line up correctly. See: http://pubs.acs.org/doi/abs/10.1021/ct300688p For ways to examine the full distribution of volumes. * Parrinello-Rahman isn't quite correct in GROMACS because virial and kinetic energy are offset by 1/2 a step, though getting something more like 1.2 atm when running at 1 atm is more common. I have been ever wondering why 1.2 and not 0.8 (from the own practice). * Note that with systems that are heterogeneous in direction (not uniform in x y and z), any errors in the pressure may be magnified. * If you have a property that changes when the pressure changes from 1 to 5 atm, odds are that molecular simulation is not the right way to study it -- the force fields are not that accurate. I believe this is not a force field problem. We calculate normal boiling points by plotting saturated vapor pressure versus temperature. The results are quite trustworthy. It is NVT simulation, of course. As the problems with simulated pressure (and conjugated properties) are, to a large extent, due to a nanoscale size of the simulated systems, it is probably worthwhile to estimate system density in certain manner and then proceed with it in the NVT. Dr. Vitaly V. Chaban On Tue, Feb 25, 2014 at 6:48 AM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: in that case the average is reasonable, but you should state in the manuscript that all the reported results correspond to 5.15 bar. Dr. Vitaly V. Chaban On Tue, Feb 25, 2014 at 10:42 AM, sujithkakkat . sujithk...@gmail.com wrote: Hi, In fact the average pressure 5.15 bar was obtained for the case where the reference pressure was 5 bar. I had mentioned it in one of the previous mails. But still the average value is not that good. I had run an earlier simulation with the same parameters for a pure water system for 5ns and reference pressure 5bar, and things worked fine there with the average pressure at 5.15bar. Sujith. On Tue, Feb 25, 2014 at 2:29 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: your average pressure is the pressure you should report in the publication. if you got 5 bars instead of 1 bar, you should write I simulated the system at 5 bars Dr. Vitaly V. Chaban On Tue, Feb 25, 2014 at 6:01 AM, sujithkakkat . sujithk...@gmail.com wrote: On Mon, Feb 24, 2014 at 5:37 AM, sujithkakkat . sujithk...@gmail.com wrote: Hello, Thank you both for the comments. I am using gromos96 forcefield . I read a little bit and as you said the nonbonded cutoff has to be higher. The tau_p=5ps was chosen , since the manual mentions that the value has to be raised by 4-5 times on going from berendsen to parrinello-rahman barostat, though I did not completely follow the reasons behind it. I will try with lower values. I had run an earlier simulation with the same parameters for a pure water system for 5ns and reference pressure 5bar, and things worked fine there with the average pressure at 5.15bar. No, this average pressure is not fine. Why isn't it fine? I admit it is not very good. I guess due to huge fluctuations the average pressure is tend to vary a bit to either side of the reference value, unless I continue the equilibration for a very long time. Also the average was calculated with g_energy, which I guess considered the entire simulation, where the first few time steps, when the system is away from equilibrium, would have poor pressure values with respect to reference , which would reflect in the average pressure calculated. Also using g_analyze to calculate average pressure between different times during the simulation did not give the same value. So I am not sure if I should aim at an average pressure which is equal to the reference pressure. Thanks, Sujith. On Mon, Feb 24, 2014 at 4:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/23/14, 11:37 PM, sujithkakkat . wrote: Hello, Thank you both for the comments. I am using gromos96 forcefield . I read a little bit and as you said the nonbonded cutoff has to be higher. The tau_p=5ps was chosen , since the manual mentions that the value has to be raised by 4-5 times on going from berendsen to parrinello-rahman barostat, though I did not completely follow the reasons behind it. I will try with lower values. I had run an earlier simulation with the same parameters for a pure water system for 5ns and reference pressure 5bar, and things worked fine there with the average pressure at 5.15bar. I guess the sigma for the case of water was low and therefore the small cut-off of 0.8nm did not
Re: [gmx-users] Binning of Free Energy landscapes
On 2/25/14, 8:30 AM, Ankita Naithani wrote: Hi Justin, Thank you for your reply. I actually wanted to know that for instance if my input to g_sham were my two principal components so would the bin indexes contain the frame numbers or time points? I get 1024 bins, and so I was confused as to how exactly and what does these indexes account for. Offhand, I think the indexes refer to frame indices, but I haven't looked into that for a long time so I could be forgetting. The source code will tell you for sure, or you can determine what's going on simply by what the numbers are - the distinction between the group sizes and values printed should be apparent. -Justin Kind regards, Ankita On Tue, Feb 25, 2014 at 1:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/25/14, 4:54 AM, Ankita Naithani wrote: Hi, I was wondering as to what exactly happens during the binning of Free Energy Landscapes as generated by g_sham? I generated Free Energy Landscapes using g_sham and my Principal Components but I am trying to understand what does bin account for and how exactly does it function? It's just a histogram, with a bin width set using -bw. The first paragraph of g_sham -h describes what the calculations are. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] C-terminus residue name in Gromos43a1
Dear Justin, Thanks for your answer. However I noticed that I had made a mistake and there is no definition of NAC in GROMOS53a6, it was the .rtp file of OPLS-AA I was looking at. So defining a new residue-type in the rtp file is not as trivial as I had hoped. I followed the instructions given on the GROMACS wab page http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field and copied the gromos43a1.ff folder and the residuetypes.dat file in my local directory. I have added the following definition of NAC to the gromos43a1.ff/aminoacids.rtp file [ NAC ] [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH3 0.0 0 [ bonds ] NCAgb_20 N Hgb_2 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 and then tried again the pdb2gmx command as following and obtained this error Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Evidently I have not defined correctly my NAC residue. However, I am not sure of how to correctly define the bonds in this specific case. Could you possibly identify the error and/or point me where to find detailed information? I have already looked at the manual but haven't been able to come up with successful definition. Thank you very much. Best, Francesca pdb2gmx -f Ac_A_NHMe/Ac_A_NHMe.pdb -o Ac_A_NHMe/Ac_A_NHMe.gro -p Ac_A_NHMe/Ac_A_NHMe.top -i Ac_A_NHMe/Ac_A_NHMe.itp -n Ac_A_NHMe/Ac_A_NHMe.ndx -q Ac_A_NHMe/Ac_A_NHMe.pdb -ignh -ter :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f Ac_A_NHMe/Ac_A_NHMe.pdb InputStructure file: gro g96 pdb tpr etc. -o Ac_A_NHMe/Ac_A_NHMe.gro Output Structure file: gro g96 pdb etc. -p Ac_A_NHMe/Ac_A_NHMe.top Output Topology file -i Ac_A_NHMe/Ac_A_NHMe.itp Output Include file for topology -n Ac_A_NHMe/Ac_A_NHMe.ndx Output, Opt! Index file -q Ac_A_NHMe/Ac_A_NHMe.pdb Output, Opt! Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsepenum id_or_ter Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id or interactive -merge enum no Merge multiple chains into a single [moleculetype]: no, all or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool yes Interactive termini selection, instead of charged (default) -[no]lys bool no Interactive lysine selection, instead of charged -[no]arg bool no Interactive arginine selection, instead of charged -[no]asp bool no Interactive aspartic acid selection, instead of
[gmx-users] aMD for Gromacs?
Hello: Does anybody knows can we do Accelerated molecular dynamics (aMD, developed in Mccammon group) in Gromacs? I seldom see someone did this in Gromacs thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] C-terminus residue name in Gromos43a1
On 2/25/14, 12:56 PM, Francesca Vitalini wrote: Dear Justin, Thanks for your answer. However I noticed that I had made a mistake and there is no definition of NAC in GROMOS53a6, it was the .rtp file of OPLS-AA I was looking at. So defining a new residue-type in the rtp file is not as trivial as I had hoped. I followed the instructions given on the GROMACS wab page http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field and copied the gromos43a1.ff folder and the residuetypes.dat file in my local directory. I have added the following definition of NAC to the gromos43a1.ff/aminoacids.rtp file [ NAC ] [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH3 0.0 0 [ bonds ] NCAgb_20 N Hgb_2 You're missing a bond here, from N to -C. [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 and then tried again the pdb2gmx command as following and obtained this error Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Evidently I have not defined correctly my NAC residue. However, I am not sure of how to correctly define the bonds in this specific case. Could you possibly identify the error and/or point me where to find detailed information? I have already looked at the manual but haven't been able to come up with successful definition. You need to use pdb2gmx -ter and select None for the C-terminus, otherwise pdb2gmx tries to build a carboxylate. When it can't find the atoms it needs to do this, it fails. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] aMD for Gromacs?
On 2/25/14, 1:03 PM, Albert wrote: Hello: Does anybody knows can we do Accelerated molecular dynamics (aMD, developed in Mccammon group) in Gromacs? I seldom see someone did this in Gromacs Gromacs has flooding, which I think is similar. But as far as aMD, no. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] aMD for Gromacs?
In fact there is one major difference: metadynamics does not have dynamics! Although a recent version have dealt with it, its implementation may require some time. Anyway, it's fine if you do not care about dynamics. Francis On Wed, Feb 26, 2014 at 6:39 AM, Michael Shirts mrshi...@gmail.com wrote: Your best bet is probably something like the PLUMED plugin to do metadynamics. aMD raises up the potential if it is below a given cutoff; metadynamics puts in bumps in the potential where you have visited. There are definitely subtle differences, but the general effects are similar. On Tue, Feb 25, 2014 at 1:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/25/14, 1:03 PM, Albert wrote: Hello: Does anybody knows can we do Accelerated molecular dynamics (aMD, developed in Mccammon group) in Gromacs? I seldom see someone did this in Gromacs Gromacs has flooding, which I think is similar. But as far as aMD, no. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Zhifeng (Francis) Jing Graduate Student in Physical Chemistry School of Chemistry and Chemical Engineering Shanghai Jiao Tong University http://sun.sjtu.edu.cn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] User-defined Potentials in Gromacs
Why tabulated function cannot resolve your question? It can do anything as long as the interaction is two-body and distance-dependent. Francis On Wed, Feb 26, 2014 at 12:03 PM, cchan2242-c cchan224...@my.cityu.edu.hkwrote: Hello everyone here! Currently I want to define a user-defined potentials for the purpose of doing molecular dynamics by interaction between certain atoms only. So I'm giving up the all-atom simulation and so the previously defined potentials in Gromacs which comprehensively includes interaction between all atoms. I have looked up tabulated potential in the manual and also the suggested document, neither of them actually helps the situation. As I am trying to use potentials from another paper which is much more complicated than the form of l-j potentials. Is there any way that I can redefined the form of the potentials? Or I have to turn my potentials into the form of l-j potentials introduced in the documents then input my own parameters? Anyone had experience with this is greatly appreciated. Kevin -- View this message in context: http://gromacs.5086.x6.nabble.com/User-defined-Potentials-in-Gromacs-tp5014810.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Zhifeng (Francis) Jing Graduate Student in Physical Chemistry School of Chemistry and Chemical Engineering Shanghai Jiao Tong University http://sun.sjtu.edu.cn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] aMD for Gromacs?
Accelerated MD does not give correct dynamics either. Systems are not trapped in minima the appropriate amount of time; you can't directly map the faster movement through space back to the movement in the original space unless the cutoff energy is so low as to not really provide any advantage. I would say that both metadynamics and accelerated MD are not necessarily the most precise of names for methods out there . . . On Tue, Feb 25, 2014 at 8:28 PM, Francis Jing francij...@gmail.com wrote: In fact there is one major difference: metadynamics does not have dynamics! Although a recent version have dealt with it, its implementation may require some time. Anyway, it's fine if you do not care about dynamics. Francis On Wed, Feb 26, 2014 at 6:39 AM, Michael Shirts mrshi...@gmail.com wrote: Your best bet is probably something like the PLUMED plugin to do metadynamics. aMD raises up the potential if it is below a given cutoff; metadynamics puts in bumps in the potential where you have visited. There are definitely subtle differences, but the general effects are similar. On Tue, Feb 25, 2014 at 1:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/25/14, 1:03 PM, Albert wrote: Hello: Does anybody knows can we do Accelerated molecular dynamics (aMD, developed in Mccammon group) in Gromacs? I seldom see someone did this in Gromacs Gromacs has flooding, which I think is similar. But as far as aMD, no. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Zhifeng (Francis) Jing Graduate Student in Physical Chemistry School of Chemistry and Chemical Engineering Shanghai Jiao Tong University http://sun.sjtu.edu.cn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] difference in potenital energy on desktop and server run
Dear allI performed MD simulation of lipid bilayer on my desktop it is giving correct results and negative potential energy (~ -10^5) but when I ran the same simulation on a server using multi thread (-nt 8), It is giving positive potential energy (~ 10^5). Initially I thought it might be problem with mpi to check this I ran simulation on cluster with single thread but still potential energy is positive.Any help would be appreciated -- View this message in context: http://gromacs.5086.x6.nabble.com/difference-in-potenital-energy-on-desktop-and-server-run-tp5014813.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] aMD for Gromacs?
Thanks a lot for kind comments guys. recently I found a PNAS paper using aMD to explore the process of GPCR activation which take place at minisecond time scale: http://www.pnas.org/content/110/27/10982 it seems that it can sample mini second events, but cannot assign proper sequential time for each frame. Probably this is also a weakness of metadynamics? I am just wondering is it possible to figure out the sequence of each conformation take place in either methods? thanks Albert On 02/26/2014 06:02 AM, Michael Shirts wrote: Accelerated MD does not give correct dynamics either. Systems are not trapped in minima the appropriate amount of time; you can't directly map the faster movement through space back to the movement in the original space unless the cutoff energy is so low as to not really provide any advantage. I would say that both metadynamics and accelerated MD are not necessarily the most precise of names for methods out there . . . -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
