Re: [gmx-users] Implementing Hamiltonian replica exchange simulations
Hamilton replica exchange is implemented in GROMACS (unless it's been broken in some way). See http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy for an older tutorial, but it should be relatively straightforward to adjust to current call patterns. On Tue, Oct 15, 2019 at 8:18 AM Searle Duay wrote: > Hi Matthew, > > Thank you very much! I appreciate it. > > Best, > Searle > > On Tue, Oct 15, 2019 at 8:44 AM Matthew Fisher < > matthew.fis...@stcatz.ox.ac.uk> wrote: > > > It's possible to implement HREX-MD with the Plumed patch. A tutorial for > > it is here - https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html > > > > If you're interested in the scientific basis behind the methodology then > > take a look here > > https://www.tandfonline.com/doi/full/10.1080/00268976.2013.824126 > > > > Best, > > Matthew > > > > Matthew Fisher > > DPhil Candidate in Inorganic Chemistry (L.L.Wong Group) > > > > Inorganic Chemistry Laboratory > > South Parks Road > > Oxford > > OX1 3QR > > UNITED KINGDOM > > > > Tel (Office): +44 (0)1865 272679 > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Searle > > Duay > > Sent: 15 October 2019 12:02 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Implementing Hamiltonian replica exchange > > simulations > > > > Thank you Prof. Lemkul. I haven't seen any discussion either on doing > HREX. > > > > -Searle > > > > On Tue, Oct 15, 2019 at 5:18 AM Justin Lemkul wrote: > > > > > > > > > > > On 10/14/19 3:48 PM, Searle Duay wrote: > > > > Hi everyone, > > > > > > > > I want to do Hamiltonian replica exchange simulations on my helical > > > peptide > > > > transitioning from transmembrane state to surface-bound state. My > > > > collective variable is the angle between the z-axis and the peptide > > > helical > > > > axis. I have 30 windows with different initial configurations. Here > is > > an > > > > example of mdp file for a window: > > > > > > > > integrator = md > > > > dt = 0.002 > > > > nsteps = 5000 > > > > nstlog = 50 > > > > nstxout = 1000 > > > > nstvout = 1000 > > > > nstfout = 1000 > > > > nstcalcenergy = 100 > > > > nstenergy = 1000 > > > > ; > > > > cutoff-scheme = Verlet > > > > nstlist = 20 > > > > rlist = 1.2 > > > > coulombtype = pme > > > > rcoulomb= 1.2 > > > > vdwtype = Cut-off > > > > vdw-modifier= Force-switch > > > > rvdw_switch = 1.0 > > > > rvdw= 1.2 > > > > ; > > > > tcoupl = Nose-Hoover > > > > tc_grps = PROT MEMB SOL_ION > > > > tau_t = 1.01.01.0 > > > > ref_t = 300 300 300 > > > > ; > > > > pcoupl = Parrinello-Rahman > > > > pcoupltype = semiisotropic > > > > tau_p = 5.0 > > > > compressibility = 4.5e-5 4.5e-5 > > > > ref_p = 1.0 1.0 > > > > ; > > > > constraints = h-bonds > > > > constraint_algorithm= LINCS > > > > continuation= yes > > > > ; > > > > nstcomm = 100 > > > > comm_mode = linear > > > > comm_grps = PROT MEMB SOL_ION > > > > ; > > > > refcoord_scaling= com > > > > ; > > > > pull= yes > > > > pull_ncoords= 1 > > > > pull_ngroups= 2 > > > > pull-group1-name= n_com > > > > pull-group2-name= c_com > > > > pull-coord1-type= umbrella > > > > pull-coord1-geometry= angle-axis > > > > pull-coord1-groups = 1 2 > > > > pull-coord1-vec = 0 0 -1 > > > > pull-coord1-start = no > > > > pull-coord1-init= 3.0 > > > > pull-coord1-k = 1000.0 > > > > > > > > The mdp file for each window varies only in the pull-coord1-init > > > parameter > > > > (ranging from 3 to 90 degrees, in 3-degree intervals). Then, I grompp > > to > > > > get 30 different tpr files. > > > > > > > > This is the command that I use for running the simulations: > > > > > > > > srun --mpi=pmi2 gmx_mpi mdrun -s window.tpr -replex 1000 -multidir > > angle0 > > > > angle1 angle2 angle3 angle4 angle5 angle6 angle7 angle8 angle9 > angle10 > > > > angle11 angle12 angle13 angle14 angle15 angle16 angle17 angle18 > angle19 > > > > angle20 angle21 angle22 angle23 angle24 angle25 angle26 angle27 > angle28 > > > > angle29 -maxh 119.5 > > > > > > > > And I'm getting the following error: > > > > The properties of the 30 systems are all the same, there is nothing > to > > > > exchange > > > > > > > > I'm wondering where the error comes from. My systems should be > > different > > > > such that the target angle is
Re: [gmx-users] Implementing Hamiltonian replica exchange simulations
Hi Matthew, Thank you very much! I appreciate it. Best, Searle On Tue, Oct 15, 2019 at 8:44 AM Matthew Fisher < matthew.fis...@stcatz.ox.ac.uk> wrote: > It's possible to implement HREX-MD with the Plumed patch. A tutorial for > it is here - https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html > > If you're interested in the scientific basis behind the methodology then > take a look here > https://www.tandfonline.com/doi/full/10.1080/00268976.2013.824126 > > Best, > Matthew > > Matthew Fisher > DPhil Candidate in Inorganic Chemistry (L.L.Wong Group) > > Inorganic Chemistry Laboratory > South Parks Road > Oxford > OX1 3QR > UNITED KINGDOM > > Tel (Office): +44 (0)1865 272679 > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Searle > Duay > Sent: 15 October 2019 12:02 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Implementing Hamiltonian replica exchange > simulations > > Thank you Prof. Lemkul. I haven't seen any discussion either on doing HREX. > > -Searle > > On Tue, Oct 15, 2019 at 5:18 AM Justin Lemkul wrote: > > > > > > > On 10/14/19 3:48 PM, Searle Duay wrote: > > > Hi everyone, > > > > > > I want to do Hamiltonian replica exchange simulations on my helical > > peptide > > > transitioning from transmembrane state to surface-bound state. My > > > collective variable is the angle between the z-axis and the peptide > > helical > > > axis. I have 30 windows with different initial configurations. Here is > an > > > example of mdp file for a window: > > > > > > integrator = md > > > dt = 0.002 > > > nsteps = 5000 > > > nstlog = 50 > > > nstxout = 1000 > > > nstvout = 1000 > > > nstfout = 1000 > > > nstcalcenergy = 100 > > > nstenergy = 1000 > > > ; > > > cutoff-scheme = Verlet > > > nstlist = 20 > > > rlist = 1.2 > > > coulombtype = pme > > > rcoulomb= 1.2 > > > vdwtype = Cut-off > > > vdw-modifier= Force-switch > > > rvdw_switch = 1.0 > > > rvdw= 1.2 > > > ; > > > tcoupl = Nose-Hoover > > > tc_grps = PROT MEMB SOL_ION > > > tau_t = 1.01.01.0 > > > ref_t = 300 300 300 > > > ; > > > pcoupl = Parrinello-Rahman > > > pcoupltype = semiisotropic > > > tau_p = 5.0 > > > compressibility = 4.5e-5 4.5e-5 > > > ref_p = 1.0 1.0 > > > ; > > > constraints = h-bonds > > > constraint_algorithm= LINCS > > > continuation= yes > > > ; > > > nstcomm = 100 > > > comm_mode = linear > > > comm_grps = PROT MEMB SOL_ION > > > ; > > > refcoord_scaling= com > > > ; > > > pull= yes > > > pull_ncoords= 1 > > > pull_ngroups= 2 > > > pull-group1-name= n_com > > > pull-group2-name= c_com > > > pull-coord1-type= umbrella > > > pull-coord1-geometry= angle-axis > > > pull-coord1-groups = 1 2 > > > pull-coord1-vec = 0 0 -1 > > > pull-coord1-start = no > > > pull-coord1-init= 3.0 > > > pull-coord1-k = 1000.0 > > > > > > The mdp file for each window varies only in the pull-coord1-init > > parameter > > > (ranging from 3 to 90 degrees, in 3-degree intervals). Then, I grompp > to > > > get 30 different tpr files. > > > > > > This is the command that I use for running the simulations: > > > > > > srun --mpi=pmi2 gmx_mpi mdrun -s window.tpr -replex 1000 -multidir > angle0 > > > angle1 angle2 angle3 angle4 angle5 angle6 angle7 angle8 angle9 angle10 > > > angle11 angle12 angle13 angle14 angle15 angle16 angle17 angle18 angle19 > > > angle20 angle21 angle22 angle23 angle24 angle25 angle26 angle27 angle28 > > > angle29 -maxh 119.5 > > > > > > And I'm getting the following error: > > > The properties of the 30 systems are all the same, there is nothing to > > > exchange > > > > > > I'm wondering where the error comes from. My systems should be > different > > > such that the target angle is different in each window. I'm not sure > if I > > > am giving the correct input to GROMACS. > > > > There is no topological difference in your systems and the Hamiltonians > > are all the same, so mdrun won't perform any kind of exchange between > > the different simulations. The manual says HREX is supported but I have > > never seen much discussion on how to make it work. It will be a > > lambda-dependent process, however, since that's the only way to alter > > the Hamiltonian of each subsystem. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > >
Re: [gmx-users] Implementing Hamiltonian replica exchange simulations
It's possible to implement HREX-MD with the Plumed patch. A tutorial for it is here - https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html If you're interested in the scientific basis behind the methodology then take a look here https://www.tandfonline.com/doi/full/10.1080/00268976.2013.824126 Best, Matthew Matthew Fisher DPhil Candidate in Inorganic Chemistry (L.L.Wong Group) Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UNITED KINGDOM Tel (Office): +44 (0)1865 272679 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Searle Duay Sent: 15 October 2019 12:02 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Implementing Hamiltonian replica exchange simulations Thank you Prof. Lemkul. I haven't seen any discussion either on doing HREX. -Searle On Tue, Oct 15, 2019 at 5:18 AM Justin Lemkul wrote: > > > On 10/14/19 3:48 PM, Searle Duay wrote: > > Hi everyone, > > > > I want to do Hamiltonian replica exchange simulations on my helical > peptide > > transitioning from transmembrane state to surface-bound state. My > > collective variable is the angle between the z-axis and the peptide > helical > > axis. I have 30 windows with different initial configurations. Here is an > > example of mdp file for a window: > > > > integrator = md > > dt = 0.002 > > nsteps = 5000 > > nstlog = 50 > > nstxout = 1000 > > nstvout = 1000 > > nstfout = 1000 > > nstcalcenergy = 100 > > nstenergy = 1000 > > ; > > cutoff-scheme = Verlet > > nstlist = 20 > > rlist = 1.2 > > coulombtype = pme > > rcoulomb= 1.2 > > vdwtype = Cut-off > > vdw-modifier= Force-switch > > rvdw_switch = 1.0 > > rvdw= 1.2 > > ; > > tcoupl = Nose-Hoover > > tc_grps = PROT MEMB SOL_ION > > tau_t = 1.01.01.0 > > ref_t = 300 300 300 > > ; > > pcoupl = Parrinello-Rahman > > pcoupltype = semiisotropic > > tau_p = 5.0 > > compressibility = 4.5e-5 4.5e-5 > > ref_p = 1.0 1.0 > > ; > > constraints = h-bonds > > constraint_algorithm= LINCS > > continuation= yes > > ; > > nstcomm = 100 > > comm_mode = linear > > comm_grps = PROT MEMB SOL_ION > > ; > > refcoord_scaling= com > > ; > > pull= yes > > pull_ncoords= 1 > > pull_ngroups= 2 > > pull-group1-name= n_com > > pull-group2-name= c_com > > pull-coord1-type= umbrella > > pull-coord1-geometry= angle-axis > > pull-coord1-groups = 1 2 > > pull-coord1-vec = 0 0 -1 > > pull-coord1-start = no > > pull-coord1-init= 3.0 > > pull-coord1-k = 1000.0 > > > > The mdp file for each window varies only in the pull-coord1-init > parameter > > (ranging from 3 to 90 degrees, in 3-degree intervals). Then, I grompp to > > get 30 different tpr files. > > > > This is the command that I use for running the simulations: > > > > srun --mpi=pmi2 gmx_mpi mdrun -s window.tpr -replex 1000 -multidir angle0 > > angle1 angle2 angle3 angle4 angle5 angle6 angle7 angle8 angle9 angle10 > > angle11 angle12 angle13 angle14 angle15 angle16 angle17 angle18 angle19 > > angle20 angle21 angle22 angle23 angle24 angle25 angle26 angle27 angle28 > > angle29 -maxh 119.5 > > > > And I'm getting the following error: > > The properties of the 30 systems are all the same, there is nothing to > > exchange > > > > I'm wondering where the error comes from. My systems should be different > > such that the target angle is different in each window. I'm not sure if I > > am giving the correct input to GROMACS. > > There is no topological difference in your systems and the Hamiltonians > are all the same, so mdrun won't perform any kind of exchange between > the different simulations. The manual says HREX is supported but I have > never seen much discussion on how to make it work. It will be a > lambda-dependent process, however, since that's the only way to alter > the Hamiltonian of each subsystem. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.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
Re: [gmx-users] Implementing Hamiltonian replica exchange simulations
Thank you Prof. Lemkul. I haven't seen any discussion either on doing HREX. -Searle On Tue, Oct 15, 2019 at 5:18 AM Justin Lemkul wrote: > > > On 10/14/19 3:48 PM, Searle Duay wrote: > > Hi everyone, > > > > I want to do Hamiltonian replica exchange simulations on my helical > peptide > > transitioning from transmembrane state to surface-bound state. My > > collective variable is the angle between the z-axis and the peptide > helical > > axis. I have 30 windows with different initial configurations. Here is an > > example of mdp file for a window: > > > > integrator = md > > dt = 0.002 > > nsteps = 5000 > > nstlog = 50 > > nstxout = 1000 > > nstvout = 1000 > > nstfout = 1000 > > nstcalcenergy = 100 > > nstenergy = 1000 > > ; > > cutoff-scheme = Verlet > > nstlist = 20 > > rlist = 1.2 > > coulombtype = pme > > rcoulomb= 1.2 > > vdwtype = Cut-off > > vdw-modifier= Force-switch > > rvdw_switch = 1.0 > > rvdw= 1.2 > > ; > > tcoupl = Nose-Hoover > > tc_grps = PROT MEMB SOL_ION > > tau_t = 1.01.01.0 > > ref_t = 300 300 300 > > ; > > pcoupl = Parrinello-Rahman > > pcoupltype = semiisotropic > > tau_p = 5.0 > > compressibility = 4.5e-5 4.5e-5 > > ref_p = 1.0 1.0 > > ; > > constraints = h-bonds > > constraint_algorithm= LINCS > > continuation= yes > > ; > > nstcomm = 100 > > comm_mode = linear > > comm_grps = PROT MEMB SOL_ION > > ; > > refcoord_scaling= com > > ; > > pull= yes > > pull_ncoords= 1 > > pull_ngroups= 2 > > pull-group1-name= n_com > > pull-group2-name= c_com > > pull-coord1-type= umbrella > > pull-coord1-geometry= angle-axis > > pull-coord1-groups = 1 2 > > pull-coord1-vec = 0 0 -1 > > pull-coord1-start = no > > pull-coord1-init= 3.0 > > pull-coord1-k = 1000.0 > > > > The mdp file for each window varies only in the pull-coord1-init > parameter > > (ranging from 3 to 90 degrees, in 3-degree intervals). Then, I grompp to > > get 30 different tpr files. > > > > This is the command that I use for running the simulations: > > > > srun --mpi=pmi2 gmx_mpi mdrun -s window.tpr -replex 1000 -multidir angle0 > > angle1 angle2 angle3 angle4 angle5 angle6 angle7 angle8 angle9 angle10 > > angle11 angle12 angle13 angle14 angle15 angle16 angle17 angle18 angle19 > > angle20 angle21 angle22 angle23 angle24 angle25 angle26 angle27 angle28 > > angle29 -maxh 119.5 > > > > And I'm getting the following error: > > The properties of the 30 systems are all the same, there is nothing to > > exchange > > > > I'm wondering where the error comes from. My systems should be different > > such that the target angle is different in each window. I'm not sure if I > > am giving the correct input to GROMACS. > > There is no topological difference in your systems and the Hamiltonians > are all the same, so mdrun won't perform any kind of exchange between > the different simulations. The manual says HREX is supported but I have > never seen much discussion on how to make it work. It will be a > lambda-dependent process, however, since that's the only way to alter > the Hamiltonian of each subsystem. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.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. > -- Searle Aichelle S. Duay Ph.D. Student Chemistry Department, University of Connecticut searle.d...@uconn.edu -- 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] Implementing Hamiltonian replica exchange simulations
On 10/14/19 3:48 PM, Searle Duay wrote: Hi everyone, I want to do Hamiltonian replica exchange simulations on my helical peptide transitioning from transmembrane state to surface-bound state. My collective variable is the angle between the z-axis and the peptide helical axis. I have 30 windows with different initial configurations. Here is an example of mdp file for a window: integrator = md dt = 0.002 nsteps = 5000 nstlog = 50 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; tcoupl = Nose-Hoover tc_grps = PROT MEMB SOL_ION tau_t = 1.01.01.0 ref_t = 300 300 300 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = PROT MEMB SOL_ION ; refcoord_scaling= com ; pull= yes pull_ncoords= 1 pull_ngroups= 2 pull-group1-name= n_com pull-group2-name= c_com pull-coord1-type= umbrella pull-coord1-geometry= angle-axis pull-coord1-groups = 1 2 pull-coord1-vec = 0 0 -1 pull-coord1-start = no pull-coord1-init= 3.0 pull-coord1-k = 1000.0 The mdp file for each window varies only in the pull-coord1-init parameter (ranging from 3 to 90 degrees, in 3-degree intervals). Then, I grompp to get 30 different tpr files. This is the command that I use for running the simulations: srun --mpi=pmi2 gmx_mpi mdrun -s window.tpr -replex 1000 -multidir angle0 angle1 angle2 angle3 angle4 angle5 angle6 angle7 angle8 angle9 angle10 angle11 angle12 angle13 angle14 angle15 angle16 angle17 angle18 angle19 angle20 angle21 angle22 angle23 angle24 angle25 angle26 angle27 angle28 angle29 -maxh 119.5 And I'm getting the following error: The properties of the 30 systems are all the same, there is nothing to exchange I'm wondering where the error comes from. My systems should be different such that the target angle is different in each window. I'm not sure if I am giving the correct input to GROMACS. There is no topological difference in your systems and the Hamiltonians are all the same, so mdrun won't perform any kind of exchange between the different simulations. The manual says HREX is supported but I have never seen much discussion on how to make it work. It will be a lambda-dependent process, however, since that's the only way to alter the Hamiltonian of each subsystem. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation
On 10/14/19 11:54 PM, ISHRAT JAHAN wrote: Go through at the following link. Hope it will resolve the issue- http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html Please update your bookmarks. That site is wildly outdated and will be taken offline soon. Use the tutorial at http://www.mdtutorials.com/gmx/complex/index.html instead. -Justin On Tue, Oct 15, 2019 at 7:26 AM Jorden Cabal wrote: Dear Amit, During equilibration you add positional restraint for protein, notice that you have added positional restraint for Zn ion, nad and protein. It should not happen if you have taken the default values while generating the positional restraints in gromacs. However I would like to look to your "nvt.mdp", "posre_zn.itp" and "posre_nad.itp" files, in order to comment on it. Thank you On Sat, Oct 12, 2019 at 1:50 PM Amit Jaiswal wrote: Dear Jorden, Many thanks for your suggestions. I solved the index file problem as I created two groups namely Protein_Zn_NAD and the other being Na_Water. But when i ran NVT equilibration, the Zn ion again got displaced far away from its original position. I cannot figure out how can i constrain the Zn ion? I guess something is wrong in the topology file. I have included the last few lines of my topology file. Please have a look whenever you are free and correct me if something is mistakenly wrong. Thanks for your time and help. *; Include Position restraint file* *#ifdef POSRES* *#include "posre.itp"* *#endif* *; Include Position restraint file* *#ifdef POSRES* *#include "posre_zn.itp"* *#endif* *; Include ligand topology* *#include "nad.itp"* *; Ligand position restraints* *#ifdef POSRES_LIG* *#include "posre_nad.itp"* *#endif* *; Include water topology* *#include "./charmm36-mar2019.ff/tip3p.itp"* *#ifdef POSRES_WATER* *; Position restraint for each water oxygen* *[ position_restraints ]* *; i funct fcx fcy fcz* *1 1 1000 1000 1000* *#endif* *; Include topology for ions* *#include "./charmm36-mar2019.ff/ions.itp"* *[ system ]* *; Name* *Protein in water* *[ molecules ]* *; Compound #mols* *Protein_chain_A 1* *ZN 1* *NAD 1* *SOL 12908* *NA 4* With kind regards, Amit 11.10.2019, 18:10, "Jorden Cabal" : Dear Amit, Please check if the Zn ion is included in both the groups declared for temperature coupling. If you notice that it is is included, you can simply create a group of all the atoms which is not in "Protein_NAD" group. You can do this by using "!group_number" as far as I remember. Then try this, it should work. Please mail if the problem persists. Thank you and all the best. -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
