[gmx-users] Running Replica Exchange with Solute Tempering (REST2) with CHARMM36M
Hello dear users, I am trying to figure out how to run Replica Exchange with Solute Tempering (REST2) simulation using CHARMM 36m force filed. The only method that I found so far involves using Plumed (which would have worked for me). However, the instructions I found ( https://plumed.github.io/doc-v2.4/user-doc/html/hrex.html) explicitly say that it will not work with CHARMM cmap. Thus, I was wondering if anyone knows an alternative method of run REST2 simulations in GROMACS in general or how to solve the cmap problem mentioned in the instructions. Thank you in advance, Aram -- 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] Running Replica Exchange with Solute Tempering (REST2) with CHARMM36M
Hello, I am trying to figure out how to run Replica Exchange with Solute Tempering (REST2) simulation using CHARMM 36m force filed. The only method that I found so far involves using Plumed (which would have worked for me). However, the instructions I found ( https://plumed.github.io/doc-v2.4/user-doc/html/hrex.html) explicitly say that it will not work with CHARMM cmap. Thus, I was wondering if anyone knows an alternative method of run REST2 simulations in GROMACS in general or how to solve the cmap problem mentioned in the instructions. Also, if anyone knows anything about parallel continuous simulated tempering (PCST) implementation in GROMACS that can also be helpful. Thank you in advance, Aram -- 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] The sum of the two largest charge group radii (32.555389) is larger than rlist
Hello, I am trying to switch my simulations from using Verlet cutoff scheme to Group. To do this I replace "cutoff-scheme = Verlet" with "cutoff-scheme = Group" and "rlist = 1.2" with "rlist = 1.4". As a result GROMACS gives me the following warning when I try to generate the tpr file with grompp, that halts the execution. WARNING 1 [file md_energygrp-table_group.mdp]: The sum of the two largest charge group radii (32.555389) is larger than rlist (1.40) Does anyone know what this means and how to deal with it? I am running a protein system with water and ions. Thank you in advance, Aram -- 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] Using custom potential for electrostatics between protein and water
Ok, so I tried the following. I have changed cutoff-scheme=verlet" to "cutoff-scheme=group" and "rlist = 1.2" to "rlist = 1.4". Now I get the following working when trying to generate the TPR: WARNING 1 [file md_energygrp-table_group.mdp]: The sum of the two largest charge group radii (32.555389) is larger than rlist (1.40) Thanks, Aram Hi Arm, > > > As mark suggested you have to replace "cutoff-scheme=verlet" to > "cutoff-scheme=group". > > > Srinivasa > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Aram > Davtyan <davtyan.a...@gmail.com> > Sent: 06 December 2017 13:57:17 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Using custom potential for electrostatics between > protein and water > > Hi, > > Yeah, but first of all it doesn't give me an error and, second, how do I > transition from verlet to group cutoff scheme in order for the custom > tables to work? > > In other words, what specific changes should I make for GROMACS to use the > modified tables, and, at the same time, when the > `table6-12_Protein_Water.xvg` is the same as `table6-12.xvg` I get the same > answer as before? > > Thanks, > > Aram > > > > > Hi, > > > > User tables for nonbonded interactions, including pme-user are only > > supported with the group cutoff scheme, not verlet. grompp should give a > > fatal error to tell you that, sorry. > > > > Mark > > > > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan <davtyan.a...@gmail.com> > > wrote: > > > > > Hello, > > > > > > I am trying to use a custom electrostatic potential between protein and > > > water, with protein-protein and water-water potentials remaining the > > same. > > > > > > I tried running the simulation with the following input script: > > > > > > define = -DPOSRES ; position restrain for protein > > > integrator = md > > > dt = 0.002 > > > nsteps = 1 ; 2ns > > > nstlog = 1000 > > > nstxout = 5000 > > > nstvout = 5000 > > > nstfout = 5000 > > > nstcalcenergy = 100 > > > nstenergy = 1000 > > > ; > > > cutoff-scheme = Verlet > > > nstlist = 20 > > > rlist = 1.2 > > > coulombtype = pme-user > > > rcoulomb= 1.2 > > > vdwtype = Cut-off > > > vdw-modifier= Force-switch > > > rvdw_switch = 1.0 > > > rvdw= 1.2 > > > ; > > > energygrps = Protein Water Ion > > > energygrp-table = Protein Water > > > ; > > > tcoupl = Nose-Hoover > > > tc_grps = Protein Non-Protein > > > tau_t = 1.0 1.0 > > > ref_t = 300.0 300.0 > > > ; > > > pcoupl = Parrinello-Rahman > > > pcoupltype = isotropic > > > tau_p = 5.0 > > > compressibility = 4.5e-5 > > > ref_p = 1.0 > > > ; > > > ld_seed = 0 > > > ; > > > constraints = h-bonds > > > constraint_algorithm= LINCS > > > continuation= yes > > > ; > > > nstcomm = 100 > > > comm_mode = linear > > > comm_grps = Protein Non-Protein > > > ; > > > refcoord_scaling= com > > > > > > I have the following tables: `table6-12.xvg` and > > > `table6-12_Protein_Water.xvg` in the directory and run the simulation > > with > > > the following command lines > > > > > > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top > > -o > > > md_0_5.tpr > > > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep > > table6-12.xvg > > > > > > To test I set the electrostatic potential (f(r) and f'(r)) to zero in > > > `table6-12_Protein_Water.xvg` file. However, I find that the energies > > > calculated at the first step are identical to the case when custom > > > potentials are not used. What am I doing wrong? > > > > > > Thank you in advance, > > > > > > Aram > > > -- > > > 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. > > > > > > > > > -- > > > > Message: 5 > > Date: Wed, 06 Dec 2017 00:46:51 + > > From: Mark Abraham <mark.j.abra...@gmail.com> > > To: gmx-us...@gromacs.org > > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] Using custom potential for electrostatics > > between protein and water > > Message-ID: > >
Re: [gmx-users] Using custom potential for electrostatics between protein and water
Is that really the only thing that would need to be changed to switch from verlet to group scheme? Because to my understanding `group` works in a different way and a buffer (skin) cutoff needs to be added. But I am not at all sure how to do that. Thanks, Aram > Hi Arm, > > > As mark suggested you have to replace "cutoff-scheme=verlet" to > "cutoff-scheme=group". > > > Srinivasa > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Aram > Davtyan <davtyan.a...@gmail.com> > Sent: 06 December 2017 13:57:17 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Using custom potential for electrostatics between > protein and water > > Hi, > > Yeah, but first of all it doesn't give me an error and, second, how do I > transition from verlet to group cutoff scheme in order for the custom > tables to work? > > In other words, what specific changes should I make for GROMACS to use the > modified tables, and, at the same time, when the > `table6-12_Protein_Water.xvg` is the same as `table6-12.xvg` I get the same > answer as before? > > Thanks, > > Aram > > > > > Hi, > > > > User tables for nonbonded interactions, including pme-user are only > > supported with the group cutoff scheme, not verlet. grompp should give a > > fatal error to tell you that, sorry. > > > > Mark > > > > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan <davtyan.a...@gmail.com> > > wrote: > > > > > Hello, > > > > > > I am trying to use a custom electrostatic potential between protein and > > > water, with protein-protein and water-water potentials remaining the > > same. > > > > > > I tried running the simulation with the following input script: > > > > > > define = -DPOSRES ; position restrain for protein > > > integrator = md > > > dt = 0.002 > > > nsteps = 1 ; 2ns > > > nstlog = 1000 > > > nstxout = 5000 > > > nstvout = 5000 > > > nstfout = 5000 > > > nstcalcenergy = 100 > > > nstenergy = 1000 > > > ; > > > cutoff-scheme = Verlet > > > nstlist = 20 > > > rlist = 1.2 > > > coulombtype = pme-user > > > rcoulomb= 1.2 > > > vdwtype = Cut-off > > > vdw-modifier= Force-switch > > > rvdw_switch = 1.0 > > > rvdw= 1.2 > > > ; > > > energygrps = Protein Water Ion > > > energygrp-table = Protein Water > > > ; > > > tcoupl = Nose-Hoover > > > tc_grps = Protein Non-Protein > > > tau_t = 1.0 1.0 > > > ref_t = 300.0 300.0 > > > ; > > > pcoupl = Parrinello-Rahman > > > pcoupltype = isotropic > > > tau_p = 5.0 > > > compressibility = 4.5e-5 > > > ref_p = 1.0 > > > ; > > > ld_seed = 0 > > > ; > > > constraints = h-bonds > > > constraint_algorithm= LINCS > > > continuation= yes > > > ; > > > nstcomm = 100 > > > comm_mode = linear > > > comm_grps = Protein Non-Protein > > > ; > > > refcoord_scaling= com > > > > > > I have the following tables: `table6-12.xvg` and > > > `table6-12_Protein_Water.xvg` in the directory and run the simulation > > with > > > the following command lines > > > > > > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top > > -o > > > md_0_5.tpr > > > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep > > table6-12.xvg > > > > > > To test I set the electrostatic potential (f(r) and f'(r)) to zero in > > > `table6-12_Protein_Water.xvg` file. However, I find that the energies > > > calculated at the first step are identical to the case when custom > > > potentials are not used. What am I doing wrong? > > > > > > Thank you in advance, > > > > > > Aram > > > -- > > > 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. > > > > > > > > > -- > > > > Message: 5 > > Date: Wed, 06 Dec 2017 00:46:51 + > > From: Mark Abraham <mark.j.abra...@gmail.com> > > To: gmx-us...@gromacs.org > > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] Using custom potential for electrostatics > > between protein and water > > Message-ID: > >
Re: [gmx-users] Using custom potential for electrostatics between protein and water
Hi, Yeah, but first of all it doesn't give me an error and, second, how do I transition from verlet to group cutoff scheme in order for the custom tables to work? In other words, what specific changes should I make for GROMACS to use the modified tables, and, at the same time, when the `table6-12_Protein_Water.xvg` is the same as `table6-12.xvg` I get the same answer as before? Thanks, Aram > Hi, > > User tables for nonbonded interactions, including pme-user are only > supported with the group cutoff scheme, not verlet. grompp should give a > fatal error to tell you that, sorry. > > Mark > > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan <davtyan.a...@gmail.com> > wrote: > > > Hello, > > > > I am trying to use a custom electrostatic potential between protein and > > water, with protein-protein and water-water potentials remaining the > same. > > > > I tried running the simulation with the following input script: > > > > define = -DPOSRES ; position restrain for protein > > integrator = md > > dt = 0.002 > > nsteps = 1 ; 2ns > > nstlog = 1000 > > nstxout = 5000 > > nstvout = 5000 > > nstfout = 5000 > > nstcalcenergy = 100 > > nstenergy = 1000 > > ; > > cutoff-scheme = Verlet > > nstlist = 20 > > rlist = 1.2 > > coulombtype = pme-user > > rcoulomb= 1.2 > > vdwtype = Cut-off > > vdw-modifier= Force-switch > > rvdw_switch = 1.0 > > rvdw= 1.2 > > ; > > energygrps = Protein Water Ion > > energygrp-table = Protein Water > > ; > > tcoupl = Nose-Hoover > > tc_grps = Protein Non-Protein > > tau_t = 1.0 1.0 > > ref_t = 300.0 300.0 > > ; > > pcoupl = Parrinello-Rahman > > pcoupltype = isotropic > > tau_p = 5.0 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > ; > > ld_seed = 0 > > ; > > constraints = h-bonds > > constraint_algorithm= LINCS > > continuation= yes > > ; > > nstcomm = 100 > > comm_mode = linear > > comm_grps = Protein Non-Protein > > ; > > refcoord_scaling= com > > > > I have the following tables: `table6-12.xvg` and > > `table6-12_Protein_Water.xvg` in the directory and run the simulation > with > > the following command lines > > > > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top > -o > > md_0_5.tpr > > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep > table6-12.xvg > > > > To test I set the electrostatic potential (f(r) and f'(r)) to zero in > > `table6-12_Protein_Water.xvg` file. However, I find that the energies > > calculated at the first step are identical to the case when custom > > potentials are not used. What am I doing wrong? > > > > Thank you in advance, > > > > Aram > > -- > > 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. > > > > > -- > > Message: 5 > Date: Wed, 06 Dec 2017 00:46:51 + > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Using custom potential for electrostatics > between protein and water > Message-ID: >
[gmx-users] Using custom potential for electrostatics between protein and water
Hello, I am trying to use a custom electrostatic potential between protein and water, with protein-protein and water-water potentials remaining the same. I tried running the simulation with the following input script: define = -DPOSRES ; position restrain for protein integrator = md dt = 0.002 nsteps = 1 ; 2ns nstlog = 1000 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme-user rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; energygrps = Protein Water Ion energygrp-table = Protein Water ; tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 1.0 1.0 ref_t = 300.0 300.0 ; pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 5.0 compressibility = 4.5e-5 ref_p = 1.0 ; ld_seed = 0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein Non-Protein ; refcoord_scaling= com I have the following tables: `table6-12.xvg` and `table6-12_Protein_Water.xvg` in the directory and run the simulation with the following command lines gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_5.tpr gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep table6-12.xvg To test I set the electrostatic potential (f(r) and f'(r)) to zero in `table6-12_Protein_Water.xvg` file. However, I find that the energies calculated at the first step are identical to the case when custom potentials are not used. What am I doing wrong? Thank you in advance, Aram -- 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] Turning off electrostatics between protein and water, then protein and protein
Hi Mark, I apologize if I did not describe my problem correctly the first time, but I need the VdW interactions to stay on between all atoms at all times. I only need to turn off the electrostatic interactions between water and proteins. Thanks, Aram Hi, > > You've described the feature correctly. Whether it is useful in a study > design is another matter :-) > > Mark > > On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan <davtyan.a...@gmail.com> > wrote: > > > Hi Mark, > > > > I am not sure I understood. If I for example say "energygrp-excl = > Protein > > Water" would not I turn off all the non-bonded interactions between water > > and protein? Or did you mean something else? > > > > Thanks, > > > > Aram > > > > > > > Hi, > > > > > > In the group scheme you can turn on energy-group exclusions to get this > > > working, but of course all of those states are sampling unphysical > things > > > from a broken forcefield. That can be OK, but you will have to be able > to > > > defend that claim. > > > > > > Mark > > > > > > On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan <davtyan.a...@gmail.com> > > > wrote: > > > > > > > Hello, > > > > > > > > I am running simulations of two protein domains in tip4p water and > > 0.15M > > > > salt concentration that contain up to 650,000 atoms total. The > protein > > > > domains are separated from each other at the start of each simulation > > > and I > > > > am measuring how the distance between them changes over time. > > > > > > > > Now, I need to do the same simulations, but with electrostatics > between > > > > proteins and water turned off (with water-water, protein-protein, > > > > ion-water, ion-protein electrostatics remaining). Then I need to > repeat > > > > that, but additionally turning off electrostatics between the two > > > domains. > > > > Water-water, ion-water, ion-protein, intra-domain electrostatics > should > > > > remain on. > > > > > > > > What will be the best way to do this? > > > > > > > > I am using CHARMM27 force field and the following settings to run the > > > > production simulations: > > > > > > > > integrator = md > > > > dt = 0.002 > > > > nsteps = 100 ; 2ns > > > > nstlog = 1000 > > > > nstxout = 5000 > > > > nstvout = 5000 > > > > nstfout = 5000 > > > > 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 = Protein Non-Protein > > > > tau_t = 1.0 1.0 > > > > ref_t = 300.0 300.0 > > > > ; > > > > pcoupl = Parrinello-Rahman > > > > pcoupltype = isotropic > > > > tau_p = 5.0 > > > > compressibility = 4.5e-5 > > > > ref_p = 1.0 > > > > ; > > > > constraints = h-bonds > > > > constraint_algorithm= LINCS > > > > continuation= yes > > > > ; > > > > nstcomm = 100 > > > > comm_mode = linear > > > > comm_grps = Protein Non-Protein > > > > ; > > > > refcoord_scaling= com > > > > > > > > > > > > I have tried to use the energy groups (energygrp-table) to specify > > > > interaction tables between water and protein, where I would set the > > > > electrostatic potential to zero. However, given that energygrp-table > > and > > > > Varlet cutoff-scheme are incompatible, I could not make it work. But > it > > > is > > > >
Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein
Hi Mark, I am not sure I understood. If I for example say "energygrp-excl = Protein Water" would not I turn off all the non-bonded interactions between water and protein? Or did you mean something else? Thanks, Aram > Hi, > > In the group scheme you can turn on energy-group exclusions to get this > working, but of course all of those states are sampling unphysical things > from a broken forcefield. That can be OK, but you will have to be able to > defend that claim. > > Mark > > On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan <davtyan.a...@gmail.com> > wrote: > > > Hello, > > > > I am running simulations of two protein domains in tip4p water and 0.15M > > salt concentration that contain up to 650,000 atoms total. The protein > > domains are separated from each other at the start of each simulation > and I > > am measuring how the distance between them changes over time. > > > > Now, I need to do the same simulations, but with electrostatics between > > proteins and water turned off (with water-water, protein-protein, > > ion-water, ion-protein electrostatics remaining). Then I need to repeat > > that, but additionally turning off electrostatics between the two > domains. > > Water-water, ion-water, ion-protein, intra-domain electrostatics should > > remain on. > > > > What will be the best way to do this? > > > > I am using CHARMM27 force field and the following settings to run the > > production simulations: > > > > integrator = md > > dt = 0.002 > > nsteps = 100 ; 2ns > > nstlog = 1000 > > nstxout = 5000 > > nstvout = 5000 > > nstfout = 5000 > > 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 = Protein Non-Protein > > tau_t = 1.0 1.0 > > ref_t = 300.0 300.0 > > ; > > pcoupl = Parrinello-Rahman > > pcoupltype = isotropic > > tau_p = 5.0 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > ; > > constraints = h-bonds > > constraint_algorithm= LINCS > > continuation= yes > > ; > > nstcomm = 100 > > comm_mode = linear > > comm_grps = Protein Non-Protein > > ; > > refcoord_scaling= com > > > > > > I have tried to use the energy groups (energygrp-table) to specify > > interaction tables between water and protein, where I would set the > > electrostatic potential to zero. However, given that energygrp-table and > > Varlet cutoff-scheme are incompatible, I could not make it work. But it > is > > possible that I did something wrong. > > > > Thank you in advance, > > > > Aram > > -- > > 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] Turning off electrostatics between protein and water, then protein and protein
Hello, I am running simulations of two protein domains in tip4p water and 0.15M salt concentration that contain up to 650,000 atoms total. The protein domains are separated from each other at the start of each simulation and I am measuring how the distance between them changes over time. Now, I need to do the same simulations, but with electrostatics between proteins and water turned off (with water-water, protein-protein, ion-water, ion-protein electrostatics remaining). Then I need to repeat that, but additionally turning off electrostatics between the two domains. Water-water, ion-water, ion-protein, intra-domain electrostatics should remain on. What will be the best way to do this? I am using CHARMM27 force field and the following settings to run the production simulations: integrator = md dt = 0.002 nsteps = 100 ; 2ns nstlog = 1000 nstxout = 5000 nstvout = 5000 nstfout = 5000 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 = Protein Non-Protein tau_t = 1.0 1.0 ref_t = 300.0 300.0 ; pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 5.0 compressibility = 4.5e-5 ref_p = 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein Non-Protein ; refcoord_scaling= com I have tried to use the energy groups (energygrp-table) to specify interaction tables between water and protein, where I would set the electrostatic potential to zero. However, given that energygrp-table and Varlet cutoff-scheme are incompatible, I could not make it work. But it is possible that I did something wrong. Thank you in advance, Aram -- 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.
