Re: [gmx-users] Use NVT to mimic NVE
Thus, what is your question now? :-) The total energy must remain conserved at all times. That's it. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 2:45 AM, Johnny Lu wrote: > I tried PME and then potential-shift-verlet for Van der Waals. The energy > is still not constant in mixed precision gromacs 5.0.1 NVE run on 12 xeon > cpu without gpu. Those were nearly the last few things that I knew that I > can try in mixed precision. The system has ~165 amino acid, ~9000 water, > and 3 Cl- ion in a truncated rhombic dodecahedron box. Total energy of the > following simulation drift constantly down. This production run was a > continuation of ~300ns npt and ~300ns nvt. The PME grid was 80x80x80. > > ; Run parameters > integrator = md-vv ; leap-frog integrator > nsteps = 15000 ; 1 ns > dt = 0.0005; 0.5 fs > > ;NVE > ; nstcomm = 500 ; remove center of mass motion to reduce energy and > temp. drift. (seems less drift without this) > shake-tol = 0.01 ; shake tolerance. > verlet-buffer-tolerance = 0.0005 > > ;Output control > nstenergy = 20 ; save energies every 1.0 ps > > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation= yes ; Restarting after NVT > constraint_algorithm = lincs; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 2 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > > vdw-modifier = Potential-shift-Verlet; > > rlist = 1.1 ; short-range neighborlist cutoff (in nm) > rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) > rvdw= 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 6 ; cubic interpolation > fourierspacing = 0.1 ; grid spacing for FFT > > ; Temperature coupling is off > tcoupl = no; modified Berendsen thermostat > ; Pressure coupling is off > pcoupl = no > > refcoord_scaling = com > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr= EnerPres ; account for cut-off vdW scheme > ; Velocity generation > gen_vel = no; Velocity generation is off > cutoff-scheme = Verlet > > > I guess the energy leakage when no thermostat is used doesn't mean the > distribution of conformation is incorrect when a thermostat is used. > Since double precision run is stable while single precision is not, the > energy leakage is caused by numerical error of the computer operation and > algorithm instead of the physics or conformation of the setup. (only the > precision changed. the mdp files were the same.) > > I also guess that the majority of simulations in published paper would have > such constant drop/rise of total energy if the thermostat is switched off. > ( Is this true??? ) > > When the Amber99ff-ILDN force field is made, NPT and NVT is used, instead > of NVE [http://dx.doi.org/10.1002%2Fprot.22711] > > The Amber lipid 14 forcefield uses NPT to create the parameters. In one of > the validations, they ran NPT followed by NVE to calculate diffusion > coefficient. The tolerance was more stringent in the NVE part than the NPT > part. The plot of energy v.s. time seems to be not in the paper. [ > http://pubs.acs.org/doi/full/10.1021/ct4010307] > > Dynamics is another matter. Langevin thermostats removes momentum transfer > and changes the rate dynamics, despite it samples the canonical ensemble > ... if the system is ergodic in practice. Two different simulations can > converge, if the string of random numbers used in langevin thermostats is > the same. I'm not sure about V-rescaling. > > I agree that all thermostats and barostats likely cause some artifacts in > dynamics. > > > On Sat, Oct 11, 2014 at 5:29 PM, Dr. Vitaly Chaban > wrote: > >> Well, if it does not conserve total energy, than such a computational >> experiment is not reliable. This is a sad truth. >> >> Philosophically, you have two options here. Either you accept that >> energy leakage is significant and then you must fight against it >> (smaller time-step, double precision, constraints, etc), or -- on the >> contrary -- you say that energy loss can be neglected and proceed "as >> is". >> >> My personal rule is if the system does not lose more than 2% of total >> energy during an entire run, the result is acceptable. I can be >> criticized for this voluntary assumption, obviously. >> >> Anyway, tricks with T-coupling constitute a very bad idea in this >> case. You basically try to mask the ene
[gmx-users] Gromacs API AnalysisData Class
Hi, I am developing some personal trajectory analysis code with Gromacs API. I have a question on using the AnalysisData class. I would like to have access to the data stored in the AnalysisData object after running a single pass over all the frames in the trajectory. I don't know how to do it and where to find the stored data. For example, I extract a position vector from each frame and use setPoint to set it into AnalysisDataHandle in the function analysisFrame. After my program run through all the frames, how can I access those position vectors stored in my AnalysisData object. Thank you. Yunlong -- 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] Acetone parameters and transferability question
On 10/10/14 6:16 PM, Ioanna Styliari wrote: Dear gmx users, I am using Gromacs 4.6.5 to simulate some amphiphilic diblock copolymers (for which I have created the .rtp files) in acetone and water mixtures. I am using the GROMOS53a6 force field. At the beginning I used the Automated Topology Builder to get the acetone files and parameters but it appears that their acetone doesn't diffuse properly with water. As I was going through the literature I found that there isn't a "good" acetone model apart from one (PAC - see reference 1 below) which has been modified for the CHARMM force field. In order to test that and also other different models (for OPLS as well) and how they mix with water I transferred all their parameters (bonds angles, charges, created new atom types with appropriate LJ parameters) for the 53a6 force field, based on the fact that when Geerke et all did the 53a6ff evaluation (see reference 2) they used the two OPLS acetone models for their calculations. I am worried whether this transfer is wrong. Could you please comment on it and if you think it is, suggest what else can be done? Generally, converting from one force field to another is not a reasonable approach, because the parametrization methods are different and in some cases, things like combination rules are different between force fields. What exactly was wrong the the parameters from ATB? Was the diffusion constant wrong? Note that such properties are not target data in Gromos96 parametrization, so it would not surprise me if they didn't come out right. The parametrization methods largely revolve around targeting thermodynamic properties. Even common water models like TIP3P and SPC (against which Gromos96 was parametrized) diffuse 2-3x too fast. -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] Use NVT to mimic NVE
I tried PME and then potential-shift-verlet for Van der Waals. The energy is still not constant in mixed precision gromacs 5.0.1 NVE run on 12 xeon cpu without gpu. Those were nearly the last few things that I knew that I can try in mixed precision. The system has ~165 amino acid, ~9000 water, and 3 Cl- ion in a truncated rhombic dodecahedron box. Total energy of the following simulation drift constantly down. This production run was a continuation of ~300ns npt and ~300ns nvt. The PME grid was 80x80x80. ; Run parameters integrator = md-vv ; leap-frog integrator nsteps = 15000 ; 1 ns dt = 0.0005; 0.5 fs ;NVE ; nstcomm = 500 ; remove center of mass motion to reduce energy and temp. drift. (seems less drift without this) shake-tol = 0.01 ; shake tolerance. verlet-buffer-tolerance = 0.0005 ;Output control nstenergy = 20 ; save energies every 1.0 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs vdw-modifier = Potential-shift-Verlet; rlist = 1.1 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 6 ; cubic interpolation fourierspacing = 0.1 ; grid spacing for FFT ; Temperature coupling is off tcoupl = no; modified Berendsen thermostat ; Pressure coupling is off pcoupl = no refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off cutoff-scheme = Verlet I guess the energy leakage when no thermostat is used doesn't mean the distribution of conformation is incorrect when a thermostat is used. Since double precision run is stable while single precision is not, the energy leakage is caused by numerical error of the computer operation and algorithm instead of the physics or conformation of the setup. (only the precision changed. the mdp files were the same.) I also guess that the majority of simulations in published paper would have such constant drop/rise of total energy if the thermostat is switched off. ( Is this true??? ) When the Amber99ff-ILDN force field is made, NPT and NVT is used, instead of NVE [http://dx.doi.org/10.1002%2Fprot.22711] The Amber lipid 14 forcefield uses NPT to create the parameters. In one of the validations, they ran NPT followed by NVE to calculate diffusion coefficient. The tolerance was more stringent in the NVE part than the NPT part. The plot of energy v.s. time seems to be not in the paper. [ http://pubs.acs.org/doi/full/10.1021/ct4010307] Dynamics is another matter. Langevin thermostats removes momentum transfer and changes the rate dynamics, despite it samples the canonical ensemble ... if the system is ergodic in practice. Two different simulations can converge, if the string of random numbers used in langevin thermostats is the same. I'm not sure about V-rescaling. I agree that all thermostats and barostats likely cause some artifacts in dynamics. On Sat, Oct 11, 2014 at 5:29 PM, Dr. Vitaly Chaban wrote: > Well, if it does not conserve total energy, than such a computational > experiment is not reliable. This is a sad truth. > > Philosophically, you have two options here. Either you accept that > energy leakage is significant and then you must fight against it > (smaller time-step, double precision, constraints, etc), or -- on the > contrary -- you say that energy loss can be neglected and proceed "as > is". > > My personal rule is if the system does not lose more than 2% of total > energy during an entire run, the result is acceptable. I can be > criticized for this voluntary assumption, obviously. > > Anyway, tricks with T-coupling constitute a very bad idea in this > case. You basically try to mask the energy leakage problem with the > thermostat. Thermostat never removes the problem itself. > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sat, Oct 11, 2014 at 11:12 PM, Johnny Lu > wrote: > > I tried NVE on single precision gromacs 4.6.7 with and without GPU. > > The energy either drift down or up, depending on the mdp file, and the > drift > > seems linear. > > > > Linear
Re: [gmx-users] Lithium Ions in Gromos53A6
What about taking another alkali ion (are thery any in CROMOS53?) and adjusting sigma&epsilon to reflect smaller size of Li(+)? Of course, lithium is a pretty polarizable guy with certain covalent bonding ambitions, but this does not prevent people to simulate it as a hard [+1e] sphere... Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Mon, Oct 6, 2014 at 2:57 PM, Hardy, Adam wrote: > Dear All, > > I find myself requiring lithium ions in a simulation using (a variant of) the > Gromos53A6 forcefield. > > Chaging forcefields is not an appealing proposition due to the time already > invested in the current one, so I was wondering had any suggestions or has > perhaps gone to the effort of creating parameters for it? > > Thanks, > > Adam Hardy > PhD Student > School of Engineering and Physical Sciences > Heriot-Watt University > Edinburgh EH14 4AS, UK > > > - > We invite research leaders and ambitious early career researchers to > join us in leading and driving research in key inter-disciplinary themes. > Please see www.hw.ac.uk/researchleaders for further information and how > to apply. > > Heriot-Watt University is a Scottish charity > registered under charity number SC000278. > > -- > 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] Use NVT to mimic NVE
Well, if it does not conserve total energy, than such a computational experiment is not reliable. This is a sad truth. Philosophically, you have two options here. Either you accept that energy leakage is significant and then you must fight against it (smaller time-step, double precision, constraints, etc), or -- on the contrary -- you say that energy loss can be neglected and proceed "as is". My personal rule is if the system does not lose more than 2% of total energy during an entire run, the result is acceptable. I can be criticized for this voluntary assumption, obviously. Anyway, tricks with T-coupling constitute a very bad idea in this case. You basically try to mask the energy leakage problem with the thermostat. Thermostat never removes the problem itself. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sat, Oct 11, 2014 at 11:12 PM, Johnny Lu wrote: > I tried NVE on single precision gromacs 4.6.7 with and without GPU. > The energy either drift down or up, depending on the mdp file, and the drift > seems linear. > > Linear fit says that if I run 100 ns simulation, at the end the energy is > doubled. > > If I use double precision gromacs, the drift seems insignificant over 100 ns > simulation by linear regression fitting on a 300 ps run. > But double precision gromacs can't use gpu and is much slower than single > precision gromacs. > > On Sat, Oct 11, 2014 at 4:33 PM, Dr. Vitaly Chaban > wrote: >> >> I also cannot get why not to just turn off the thermostat... >> >> If energy transfer phenomena are in focus, NVE is an ensemble of >> choice, no matter which relaxation constant is used for the T-coupling >> algorithm. >> >> >> Dr. Vitaly V. Chaban >> >> Виталий Витальевич ЧАБАН >> >> >> On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista >> wrote: >> > Then, run true NVE, for the reasons we already pointed. >> > >> > On Sat, 11 Oct 2014, Johnny Lu wrote: >> > >> >> For dynamics with correct rate and correct fluctuation. >> >> >> >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban >> >> wrote: >> >> >> >>> what is it needed for? >> >>> >> >>> >> >>> >> >>> Dr. Vitaly V. Chaban >> >>> >> >>> Виталий Витальевич ЧАБАН >> >>> >> >>> >> >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu >> >>> wrote: >> >>> > Hi. >> >>> > >> >>> > Is it a good idea to mimic NVE by a NVT simulation with a large >> >>> temperature >> >>> > coupling time constant, to reduce the effect of the thermostat ? >> >>> > >> >>> > If I use V-rescale thermostat, what artifacts will the simulation >> >>> > get >> >>> > if >> >>> I >> >>> > use a large coupling time (say, 500 ps) and single precision gromacs >> >>> > ? >> >>> > >> >>> > Thank you. >> >>> > -- >> >>> > 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. >> >>> >> >> -- >> >> 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. >> > >> -- >> 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://ww
Re: [gmx-users] Use NVT to mimic NVE
I tried NVE on single precision gromacs 4.6.7 with and without GPU. The energy either drift down or up, depending on the mdp file, and the drift seems linear. Linear fit says that if I run 100 ns simulation, at the end the energy is doubled. If I use double precision gromacs, the drift seems insignificant over 100 ns simulation by linear regression fitting on a 300 ps run. But double precision gromacs can't use gpu and is much slower than single precision gromacs. On Sat, Oct 11, 2014 at 4:33 PM, Dr. Vitaly Chaban wrote: > I also cannot get why not to just turn off the thermostat... > > If energy transfer phenomena are in focus, NVE is an ensemble of > choice, no matter which relaxation constant is used for the T-coupling > algorithm. > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista > wrote: > > Then, run true NVE, for the reasons we already pointed. > > > > On Sat, 11 Oct 2014, Johnny Lu wrote: > > > >> For dynamics with correct rate and correct fluctuation. > >> > >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban > >> wrote: > >> > >>> what is it needed for? > >>> > >>> > >>> > >>> Dr. Vitaly V. Chaban > >>> > >>> Виталий Витальевич ЧАБАН > >>> > >>> > >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu > >>> wrote: > >>> > Hi. > >>> > > >>> > Is it a good idea to mimic NVE by a NVT simulation with a large > >>> temperature > >>> > coupling time constant, to reduce the effect of the thermostat ? > >>> > > >>> > If I use V-rescale thermostat, what artifacts will the simulation get > >>> > if > >>> I > >>> > use a large coupling time (say, 500 ps) and single precision gromacs > ? > >>> > > >>> > Thank you. > >>> > -- > >>> > 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. > >>> > >> -- > >> 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. > > > -- > 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] Use NVT to mimic NVE
I also cannot get why not to just turn off the thermostat... If energy transfer phenomena are in focus, NVE is an ensemble of choice, no matter which relaxation constant is used for the T-coupling algorithm. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista wrote: > Then, run true NVE, for the reasons we already pointed. > > On Sat, 11 Oct 2014, Johnny Lu wrote: > >> For dynamics with correct rate and correct fluctuation. >> >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban >> wrote: >> >>> what is it needed for? >>> >>> >>> >>> Dr. Vitaly V. Chaban >>> >>> Виталий Витальевич ЧАБАН >>> >>> >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu >>> wrote: >>> > Hi. >>> > >>> > Is it a good idea to mimic NVE by a NVT simulation with a large >>> temperature >>> > coupling time constant, to reduce the effect of the thermostat ? >>> > >>> > If I use V-rescale thermostat, what artifacts will the simulation get >>> > if >>> I >>> > use a large coupling time (say, 500 ps) and single precision gromacs ? >>> > >>> > Thank you. >>> > -- >>> > 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. >>> >> -- >> 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. > -- 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] Use NVT to mimic NVE
Then, run true NVE, for the reasons we already pointed. On Sat, 11 Oct 2014, Johnny Lu wrote: For dynamics with correct rate and correct fluctuation. On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban wrote: what is it needed for? Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: > Hi. > > Is it a good idea to mimic NVE by a NVT simulation with a large temperature > coupling time constant, to reduce the effect of the thermostat ? > > If I use V-rescale thermostat, what artifacts will the simulation get if I > use a large coupling time (say, 500 ps) and single precision gromacs ? > > Thank you. > -- > 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. -- 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] Use NVT to mimic NVE
For dynamics with correct rate and correct fluctuation. On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban wrote: > what is it needed for? > > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: > > Hi. > > > > Is it a good idea to mimic NVE by a NVT simulation with a large > temperature > > coupling time constant, to reduce the effect of the thermostat ? > > > > If I use V-rescale thermostat, what artifacts will the simulation get if > I > > use a large coupling time (say, 500 ps) and single precision gromacs ? > > > > Thank you. > > -- > > 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. > -- 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] Use NVT to mimic NVE
Following up on fluctuations and ensembles: The following paper discusses tests of whether an ensemble has the correct distribution of energies, including fluctuations of all scale: "Simple quantitative tests to validate sampling from thermodynamic ensembles" http://pubs.acs.org/doi/abs/10.1021/ct300688p Turns out that v-rescale behaves very well, at least for fluctuations of the total energy. In the limit of large scale, for NVE and NVT (if carried out at the temperature where _NVT = E_NVE, then all system averages (including pressure, etc) will be equal. But the fluctuations (which include 2nd derivative properties like heat capacity, etc). will not be equal. So it depends on what you are interested in. If you are interested in thermodynamics, just go ahead and run the ensemble you are interested in. If you are interested in dynamics, you can check out this paper which partly answers the questions of what the artifacts are created by thermostats. Again, vrescale is quite good -- Langevin or anything with stochastic noise is not so good. "Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations" http://pubs.acs.org/doi/abs/10.1021/ct400109a Best, Michael Shirts Associate Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 On Fri, Oct 10, 2014 at 7:40 PM, Antonio Baptista wrote: > On Fri, 10 Oct 2014, Mark Abraham wrote: > > On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu >> wrote: >> >> Hi. >>> >>> Is it a good idea to mimic NVE by a NVT simulation with a large >>> temperature >>> coupling time constant, to reduce the effect of the thermostat ? >>> >>> >> Not if your observable is the total energy. But for most interesting >> observables, this is more than fine. >> >> >> If I use V-rescale thermostat, what artifacts will the simulation get if >>> I >>> use a large coupling time (say, 500 ps) and single precision gromacs ? >>> >>> >> Probably nobody knows :-) Thermodynamic ensemble differences disappear as >> the system becomes large. But quantifying that from converged ensembles >> for >> a given observable is work. >> >> Mark >> > > Note also that, unlike averages, fluctuations are ensemble-dependent. > Although v-rescaling (as most other thermostats) does indeed sample from > the NVE ensemble in the mathematical limit of infinite coupling constant, > this does not imply that, in practice, fluctuations converge to those in > the NVE ensemble for large but finite coupling constants. > > As you can check in the v-rescaling paper, fluctuations were found to be > very robust to changes of the coupling parameter (at least for the kinetic > and potential energies). This is generally a good thing, but maybe not what > you want to run a "fake" NVE simulation as you described. So, if you are > interested in the fluctuations of some properties, you will have to check > what is in practice their asymptotic behavior. > > Best, > Antonio > > > > >> >> Thank you. >>> -- >>> 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. >> >> -- > 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] Use NVT to mimic NVE
what is it needed for? Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: > Hi. > > Is it a good idea to mimic NVE by a NVT simulation with a large temperature > coupling time constant, to reduce the effect of the thermostat ? > > If I use V-rescale thermostat, what artifacts will the simulation get if I > use a large coupling time (say, 500 ps) and single precision gromacs ? > > Thank you. > -- > 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.
