[gmx-users] Non-integer charges when using scaled-topology files for REST2 simulation.
Dear Gromacs users. While creating the .tpr files for a hamiltonian replex, I noticed that the grompp gives a note regarding Non-integer charges in case of the replicas with scaled potentials. I do not get such a note in case of the unscaled replica. My concern is that the charge values are deviating too much from neutral charge. Example of some charges grompp calculated are 0.047129, 0.093166, 0.817435, 0.845293 etc. Such numbers generally indicate a problem with topology, but should this be a big concern in case of REST2 simulations? Thank you Regards, Abhishek -- 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] NVE Energy drop in Mixed Precision 4.6.7
Hi, You should maybe show us a plot of the energy for more than just a few picoseconds. Nevertheless, from my experience the only way to obtain constant energy in the NVE ensemblewas to use double precision. Guillaume On 10/06/2014 09:34 PM, Johnny Lu wrote: The run was on 12 Xeon CPU with a GPU. On Mon, Oct 6, 2014 at 3:03 PM, Johnny Lu wrote: here is the energy from nve1.edr http://oi62.tinypic.com/2pqw70l.jpg On Mon, Oct 6, 2014 at 3:01 PM, Johnny Lu wrote: Hi. The system has 9000 water and a ~160 aa amino acid and uses amber99SB-ildn. After extensive NPT (300ns, 2ns ts), and then NVT equilibrium (300 ns, 2ns ts), the NVE simulation still has energy drop, despite of the very small time step. Is double precision gromacs the only solution? The mdp file is: title = NVT equilibration ; Run parameters integrator = md; leap-frog integrator nsteps = 2950 ; 1 ns dt = 0.0002; 0.5 fs ;NVE ;nstcomm = 500 ; remove center of mass motion to reduce energy and temp. drift. shake-tol = 0.001 ; shake tolerance. verlet-buffer-drift = -1 - Output control ;nstxout = 20 ; save coordinates every 1.0 ps ;nstvout = 4 ; save velocities every 1.0 ps ;nstfout= 20 nstenergy = 20 ; save energies every 1.0 ps nstlog = 1000 ; 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 = 4 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 40; 10 fs rlist = 1.3 ; 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 Thank you in advance. -- 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] Non-integer charges when using scaled-topology files for REST2 simulation.
Hello, Thank you for replying. I have also come across a note on this issue in the following link: https://github.com/GiovanniBussi/plumed2/blob/v2.0-hrex/user-doc/tutorials/hrex.txt It says that Gromacs takes care of this by adding a compensating background, though I am not sure how exactly is this compensation achieved. Any ideas? Regards, Abhishek On Tue, Oct 7, 2014 at 1:40 PM, Scott Dean wrote: > Hey Abhi, > > I've gotten REST2 simulations working well in gromacs. So far, only the > -maxwarn flag has been needed... Not that ignoring the issue is the best > way of doing things, but the trajectories appear to be correct and > replicating the TrpCage example from the Wang et al., 2011 paper has been > possible. > > Scott > -- 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] Non-integer charges when using scaled-topology files for REST2 simulation.
I recently asked a similar question in a different forum and was led to this paper: Heyes, D. M. (1981). Electrostatic potentials and fields in infinite point charge lattices. *The Journal of Chemical Physics*, *74*(3), 1924-1929. But I'm afraid I didn't finish reading/understanding it. Maybe now I will. Scott On Tue, Oct 7, 2014 at 5:10 AM, Abhi Acharya wrote: > Hello, > > Thank you for replying. > > I have also come across a note on this issue in the following link: > > > https://github.com/GiovanniBussi/plumed2/blob/v2.0-hrex/user-doc/tutorials/hrex.txt > > It says that Gromacs takes care of this by adding a compensating > background, though I am not sure how exactly is this compensation achieved. > Any ideas? > > Regards, > Abhishek > > > On Tue, Oct 7, 2014 at 1:40 PM, Scott Dean > wrote: > >> Hey Abhi, >> >> I've gotten REST2 simulations working well in gromacs. So far, only the >> -maxwarn flag has been needed... Not that ignoring the issue is the best >> way of doing things, but the trajectories appear to be correct and >> replicating the TrpCage example from the Wang et al., 2011 paper has been >> possible. >> >> Scott >> > > -- 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] Mutation
Hi all, I am doing mutation of some ligands in water and inside the protein cavity as well and for that I chose a 3-step process to do that. 1st I do discharging and then switching the vdw's between the ligands and then in the 3rd step I do recharging again. For that I do need a four equilibrium ensemble. In the discharging step in water, I do have the 1st ligand equilibriated with charge and with non-charged and also the same for the 2nd ligand. Therefore whenever I have all those four equilibriated ensembles, I do mutate between them with the softcore potential (alpha=0.25, sigma=0.30). Now inside the protein cavity I also need the same four euilibriated ensemble. I performed the equilibration but the non-charged ligands are seems to me a bit unstable therefore I thought of taking only the state 0 and state 1 only for the mutation inside the cavity. I neglected the intermediates. I got somehow reasonable results. Since we know the non-equilibrium CGI should be started with the equilibrium ensemble therefore I am a bit nervous to do that. Could somebody direct me to do a better way or the strategy I am following, if it is okay for the simulation of mutation. thank you very much in advance. -- Susanta Haldar Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic. -- 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] Non-integer charges when using scaled-topology files for REST2 simulation.
On 2014-10-07 11:34, Scott Dean wrote: I recently asked a similar question in a different forum and was led to this paper: Heyes, D. M. (1981). Electrostatic potentials and fields in infinite point charge lattices. *The Journal of Chemical Physics*, *74*(3), 1924-1929. But I'm afraid I didn't finish reading/understanding it. Maybe now I will. Scott Using a compensating background charge is non-physical and can lead to artifacts. I personally would suggest to reject papers using it. On Tue, Oct 7, 2014 at 5:10 AM, Abhi Acharya wrote: Hello, Thank you for replying. I have also come across a note on this issue in the following link: https://github.com/GiovanniBussi/plumed2/blob/v2.0-hrex/user-doc/tutorials/hrex.txt It says that Gromacs takes care of this by adding a compensating background, though I am not sure how exactly is this compensation achieved. Any ideas? Regards, Abhishek On Tue, Oct 7, 2014 at 1:40 PM, Scott Dean wrote: Hey Abhi, I've gotten REST2 simulations working well in gromacs. So far, only the -maxwarn flag has been needed... Not that ignoring the issue is the best way of doing things, but the trajectories appear to be correct and replicating the TrpCage example from the Wang et al., 2011 paper has been possible. Scott -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] NVE Energy drop in Mixed Precision 4.6.7
Sure, there's drift. But is it significant? What is its value in units of k_B T / dof / ns? How much will such drift affect the quality of your observables? Is that more significant than your other approximations (force field parameterization targets not matching your observables, no polarization, incomplete sampling, lack of replicates)? Is fixing it worth the hit of more than a factor of two in number of samples? It's relatively easy to feel good about solving the one problem that you can solve. But only solve it if it's the one that matters ;-) Mark On Mon, Oct 6, 2014 at 9:03 PM, Johnny Lu wrote: > here is the energy from nve1.edr > http://oi62.tinypic.com/2pqw70l.jpg > > On Mon, Oct 6, 2014 at 3:01 PM, Johnny Lu wrote: > > > Hi. > > > > The system has 9000 water and a ~160 aa amino acid and uses > amber99SB-ildn. > > > > After extensive NPT (300ns, 2ns ts), and then NVT equilibrium (300 ns, > 2ns > > ts), the NVE simulation still has energy drop, despite of the very small > > time step. > > > > Is double precision gromacs the only solution? > > > > The mdp file is: > > > > title = NVT equilibration > > ; Run parameters > > integrator = md; leap-frog integrator > > nsteps = 2950 ; 1 ns > > dt = 0.0002; 0.5 fs > > > > ;NVE > > ;nstcomm = 500 ; remove center of mass motion to reduce energy > and > > temp. drift. > > shake-tol = 0.001 ; shake tolerance. > > verlet-buffer-drift = -1 > > > > > > - Output control > > ;nstxout = 20 ; save coordinates every 1.0 ps > > ;nstvout = 4 ; save velocities every 1.0 ps > > ;nstfout= 20 > > nstenergy = 20 ; save energies every 1.0 ps > > > > nstlog = 1000 ; 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 = 4 ; accuracy of LINCS > > lincs_order = 4 ; also related to accuracy > > ; Neighborsearching > > ns_type = grid ; search neighboring grid cells > > nstlist = 40; 10 fs > > rlist = 1.3 ; 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 > > > > Thank you in advance. > > > -- > 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] Regarding msd
Hi all I have created my own code for msd calculation and would like to verify it from g_msd. I have created pdb files using trjconv -center -pbc whole option. Can I use the coordinates in pdb as such (with no wrapping/unwrapping/shifting) for running my code? or does the inbuild g_msd program modifies them (shift)? My msd values are not matching with the g_msd values. I suspect that discrepency in the pdb file creation since the values obtained from my program agrees with manual calculation (of some dummy values). Any suggestions are highly welcomed. -- 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] Problem with constraints in NVT calculations.
On 10/6/14 10:35 PM, Kester Wong wrote: Dear Justin and all, 원본 메일 - *보낸사람* : Justin Lemkul *받는사람* : *받은날짜* : 2014년 9월 29일(월) 21:32:13 *제목* : Re: [gmx-users] Problem with constraints in NVT calculations. On 9/29/14 8:01 AM, Kester Wong wrote: > Dear all, > > > I have been using the SWM4-NDP water model that works well with CHARMM27 force > field. > Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive force field. The two are not compatible. If you're using them together, you're basically just gambling that they work. You shouldn't do this. Thank you for the information. Actually, I took the data from the ff-drude-water-ions.itp file and included them in the CHARMM27 itp files. Now I realised that it does not work like that. If the ffnonbonded.itp file contains the appropriate nonbonded parameters for the polarisable water model (i.e. the atomtypes and dummies for the Drude water and ions model), will it work? Below is my input topologies: https://drive.google.com/file/d/0B7ym8d6G9-e2dmdQOHNaU3c3Qkk/view?usp=sharing No, this is fundamentally wrong. You can't simply combine some additive components and some polarizable components and hope for a sensible physical model. Force fields are derived in self-consistent ways. You can't patch them together. > The force field (most recent version) was obtained from virtualchemistry, and > consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al. > > The water on graphene (energy minimisation and NVT) calculations are stable, and > have produced a few NVT runs of up to 10ns. > > I also compared the NVT runs with other previously calculated structures, > namely, the visualised NVT runs are very much comparable to that obtained by > CHARMM27 force field with TIPS3P water model. > > > However, as the polarisable H3O+ and Cl- ions are inserted into the simulation > box, the NVT run tends to crash as a result of too many LINCS warnings. > > I suspect that the constraints in the H3O is the cause of the LINCS warnings, > and after removing the [ constraints ] in the topology file, the calculation > seems to be running. > > > ;[ constraints ] > > ;; i funct doh dhh > > ;1 3 1 0.102 > > ;1 4 1 0.102 > > ;1 5 1 0.102 > > ;3 4 1 0.169124 > > ;4 5 1 0.169124 > > ;3 5 1 0.169124 > > > > Can anyone please tell me if what I am doing is correct? > > As I am not sure if removing the H3O constraints in the NVT run is appropriate. > > > With regard to the massless Drude and standard oxygen mass (thank you Justin for > providing the information), I would like to know why are they not appropriate > (as mentioned in the previous email) for the SWM4-NDP model? > I wasn't making a declarative statement that it won't work. I was asking whether anyone had verified that using a massless Drude in that model actually reproduced all of the physical properties of the SWM4-NDP model. We do all of our development on the Drude FF with Drudes of mass = 0.4 amu and the extended Lagrangian. I don't know how a massless Drude behaves in this model. It may work fine, but you should very rigorously verify this yourself before doing anything by doing simulations of pure water. -Justin I have Read the paper by Jochen Hub et al [Chem. Sci., 5, 1745 2013], that their calculated data (water with ions) are in line with experimental results. Upon further inspection, I found more papers that reported the use of 0.4 amu mass and an extended Lagrangian for the Drude particle. e.g. by Yu et al. [J. CHem. Theory Comput. 6, 774-786 2010]. Could you please advise if there is anything I could do, to make the additive and polarisable FFs usable after modification? No. Either the force field must be entirely polarizable or entirely additive. I am more than willing to go through the necessary changes/implementation if it can be done as this is the only avenue that I have left. I am working on the code-level implementation of all the necessary algorithms so people can use our fully polarizable biomolecular FFs for proteins, DNA, water, and ions. It's not a trivial task. I have only a few more hang-ups to work out, but at this point, if you want to be doing polarizable simulations with our FFs, you should look at NAMD. It supports everything you need. -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...@ou
[gmx-users] Dead inflategro.pl link?
I am working through the second tutorial from Dr. Justin A. Lemkul's tutorial site and have run into a problem finding the inflategro.pl file online. When I try the link in the tutorial I get the error: Firefox can't find the server at www.csb.bit.uni-bonn.de My network connection is fine, I tried accessing the site yesterday and today in case the server was down temporarily, and also checked Dr. Peter Tieleman's site for a copy of inflategro.pl but still cannot find this file online. Does anyone know where I can access the script? Thanks, Drew Biedermann -- 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] Dead inflategro.pl link?
On 10/7/14 4:17 PM, andrew biedermann wrote: I am working through the second tutorial from Dr. Justin A. Lemkul's tutorial site and have run into a problem finding the inflategro.pl file online. When I try the link in the tutorial I get the error: Firefox can't find the server at www.csb.bit.uni-bonn.de My network connection is fine, I tried accessing the site yesterday and today in case the server was down temporarily, and also checked Dr. Peter Tieleman's site for a copy of inflategro.pl but still cannot find this file online. Does anyone know where I can access the script? I have had to change the InflateGRO link at least once before when it moved. I may just have to distribute my own copy. Contact me off-list if the site remains down. -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.
[gmx-users] TPI calculation in desired coordinates
Dear all, I have simulate confined water between two solid crystals with infinite XY-periodic dimension. Now I want to calculate the chemical potential of the Neon atom in confined water. I think integrator=tpi option is not appropriate due to the two solids, so I am using integrator=tpic option. I have questions. 1. Is integrator=tpic option appropriate option? 2. GROMACS manual says: "The molecule to be inserted should be centered at 0,0,0” Following this manual, should I center the location of the cavity where Neon atom will be inserted to 0, 0, 0? What will happen if the location of the cavity is not 0, 0, 0? 3. tpic reads the cavity location from the trajectory. But my simulation result surely doesn’t contains Neon atom. Is there any script or g_ utility including coordinate of the Neon atom to the .trr file? Thank you. -- Kim Q Hwan Center of Nano-Liquid Department of Physics & Astronomy Seoul National University Sent with Sparrow (http://www.sparrowmailapp.com/?sig) -- 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] Problem with constraints in NVT calculations.
Hi Justin, Thank you for the clarification. I should look into using NAMD.The new polarisable Drude implementation will surely benefit everyone in the MD community.I am looking forward to using it, as with others (I think there was a similar post by Yana Tsoneva on this issue too, dated back in July).Meanwhile, is it possible to implement a self-consistent FF from scratch? One example I came across is from the work by Ho and Striolo titled: Polarizability effects in molecular dynamics simulations of the graphene-water interfacePardon me if this sounds outright wrong; regarding the massless Drude particle, can it be replaced with an atom (assuming an induced dipole model) instead of the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an opposite charge of the water oxygen atom?Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul 받는사람 : 받은날짜 : 2014년 10월 8일(수) 03:02:12제목 : Re: [gmx-users] Problem with constraints in NVT calculations. On 10/6/14 10:35 PM, Kester Wong wrote: > Dear Justin and all, > > > 원본 메일 - > > *보낸사람* : Justin Lemkul > *받는사람* : > *받은날짜* : 2014년 9월 29일(월) 21:32:13 > *제목* : Re: [gmx-users] Problem with constraints in NVT calculations. > > On 9/29/14 8:01 AM, Kester Wong wrote: > > Dear all, > > > > > > I have been using the SWM4-NDP water model that works well with CHARMM27 force > > field. > > > > Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive > force field. The two are not compatible. If you're using them together, you're > basically just gambling that they work. You shouldn't do this. > > Thank you for the information. Actually, I took the data from the > ff-drude-water-ions.itp file and included them in the CHARMM27 itp files. Now I > realised that it does not work like that. > > > If the ffnonbonded.itp file contains the appropriate nonbonded parameters for > the polarisable water model (i.e. the atomtypes and dummies for the Drude water > and ions model), will it work? > > Below is my input topologies: > > https://drive.google.com/file/d/0B7ym8d6G9-e2dmdQOHNaU3c3Qkk/view?usp=sharing No, this is fundamentally wrong. You can't simply combine some additive components and some polarizable components and hope for a sensible physical model. Force fields are derived in self-consistent ways. You can't patch them together. > > > The force field (most recent version) was obtained from virtualchemistry, and > > consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al. > > > > The water on graphene (energy minimisation and NVT) calculations are stable, and > > have produced a few NVT runs of up to 10ns. > > > > I also compared the NVT runs with other previously calculated structures, > > namely, the visualised NVT runs are very much comparable to that obtained by > > CHARMM27 force field with TIPS3P water model. > > > > > > However, as the polarisable H3O+ and Cl- ions are inserted into the simulation > > box, the NVT run tends to crash as a result of too many LINCS warnings. > > > > I suspect that the constraints in the H3O is the cause of the LINCS warnings, > > and after removing the [ constraints ] in the topology file, the calculation > > seems to be running. > > > > > > ;[ constraints ] > > > > ;; i funct doh dhh > > > > ;1 3 1 0.102 > > > > ;1 4 1 0.102 > > > > ;1 5 1 0.102 > > > > ;3 4 1 0.169124 > > > > ;4 5 1 0.169124 > > > > ;3 5 1 0.169124 > > > > > > > > Can anyone please tell me if what I am doing is correct? > > > > As I am not sure if removing the H3O constraints in the NVT run is appropriate. > > > > > > With regard to the massless Drude and standard oxygen mass (thank you Justin for > > providing the information), I would like to know why are they not appropriate > > (as mentioned in the previous email) for the SWM4-NDP model? > > > > I wasn't making a declarative statement that it won't work. I was asking > whether anyone had verified that using a massless Drude in that model actually > reproduced all of the physical properties of the SWM4-NDP model. We do all of > our development on the Drude FF with Drudes of mass = 0.4 amu and the extended > Lagrangian. I don't know how a massless Drude behaves in this model. It may > work fine, but you should very rigorously verify this yourself before doing > anything by doing simulations of pure water. > > -Justin > > I have Read the paper by Jochen Hub et al [Chem. Sci., 5, 1745 2013], that their > calculated data (water with ions) are in line with experimental results. > Upon furt
Re: [gmx-users] Non-integer charges when using scaled-topology files for REST2 simulation.
Thank you. It seems there is little choice with respect to the non-integer charges, so I will try and run the simulations. See if it works for my system. Regards, Abhishek On Tue, Oct 7, 2014 at 3:45 PM, David van der Spoel wrote: > On 2014-10-07 11:34, Scott Dean wrote: > >> I recently asked a similar question in a different forum and was led to >> this paper: Heyes, D. M. (1981). Electrostatic potentials and fields in >> infinite point charge lattices. *The Journal of Chemical Physics*, >> *74*(3), >> 1924-1929. >> >> But I'm afraid I didn't finish reading/understanding it. Maybe now I will. >> >> Scott >> >> Using a compensating background charge is non-physical and can lead to > artifacts. I personally would suggest to reject papers using it. > > >> >> On Tue, Oct 7, 2014 at 5:10 AM, Abhi Acharya >> wrote: >> >> Hello, >>> >>> Thank you for replying. >>> >>> I have also come across a note on this issue in the following link: >>> >>> >>> https://github.com/GiovanniBussi/plumed2/blob/v2. >>> 0-hrex/user-doc/tutorials/hrex.txt >>> >>> It says that Gromacs takes care of this by adding a compensating >>> background, though I am not sure how exactly is this compensation >>> achieved. >>> Any ideas? >>> >>> Regards, >>> Abhishek >>> >>> >>> On Tue, Oct 7, 2014 at 1:40 PM, Scott Dean >>> wrote: >>> >>> Hey Abhi, I've gotten REST2 simulations working well in gromacs. So far, only the -maxwarn flag has been needed... Not that ignoring the issue is the best way of doing things, but the trajectories appear to be correct and replicating the TrpCage example from the Wang et al., 2011 paper has been possible. Scott >>> >>> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > 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] Regarding msd
Please reply. Its really urgent. I have got comments from reviewer and would have to resubmit the paper. On Tue, Oct 7, 2014 at 10:03 PM, pratibha kapoor wrote: > Hi all > > I have created my own code for msd calculation and would like to verify it > from g_msd. I have created pdb files using trjconv -center -pbc whole > option. Can I use the coordinates in pdb as such (with no > wrapping/unwrapping/shifting) for running my code? or does the inbuild > g_msd program modifies them (shift)? > My msd values are not matching with the g_msd values. I suspect that > discrepency in the pdb file creation since the values obtained from my > program agrees with manual calculation (of some dummy values). > Any suggestions are highly welcomed. > -- 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] "Warning: For efficient BFGS minimization, use shift/switch/PME instead of cut-off"
> Thank you for your suggestions. I followed your instruction and applied potential modifier during energy minimization. However, the problem still persists. Please suggest what to do. > > On 9/26/14 5:34 AM, GAYATHRI S wrote: >> Hello everyone, >> >> I'm running a simulation with Verlet scheme (for GPU). >> I've used "cut-off" method for van der Waals interactions and PME for >> electrostatic interactions. For energy minimization, I used steepest >> descent, conjugate gradient and l-bfgs sequentially. However, when I >> come >> to BFGS minimization, I get the following warning: >> >> "Warning: For efficient BFGS minimization, use shift/switch/PME instead >> of >> cut-off" >> > > Did you use a suitable vdw-modifier? Perhaps some of the input checking > is > still out of whack, but if not, a suitable modifier should take care of > this. > > -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.
