Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Mark Abraham 
Hi,

You can't decompose the "turning off" in the FE code by groups. You can
turn off the coulomb in the protein, but that turns off its interactions
with itself, solvent, and anything else

Mark

On Sun, Nov 19, 2017 at 9:27 PM Justin Lemkul  wrote:

>
>
> On 11/19/17 3:42 PM, Mark Abraham wrote:
> > Hi,
> >
> > Oh, I see. Yes that feature turns off both kinds of non-bonded
> > interactions. Then there is nothing useful for what you want.
>
> Couldn't this be done with the free energy code?
>
> Turn off protein-water electrostatics by running in the lambda=1 state
> with:
>
> couple-lambda0 = vdw-q
> couple-lambda1 = vdw
> couple-intramol = no
>
> Then switch to couple-intramol = yes to turn off protein-protein
> interactions.
>
> I imagine it would be a huge memory hog and would run really slowly, but
> it's a possible solution.
>
> -Justin
>
> > Mark
> >
> > On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan 
> wrote:
> >
> >> 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 
> >>> 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  > 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

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Justin Lemkul 



On 11/19/17 3:42 PM, Mark Abraham wrote:

Hi,

Oh, I see. Yes that feature turns off both kinds of non-bonded
interactions. Then there is nothing useful for what you want.


Couldn't this be done with the free energy code?

Turn off protein-water electrostatics by running in the lambda=1 state with:

couple-lambda0 = vdw-q
couple-lambda1 = vdw
couple-intramol = no

Then switch to couple-intramol = yes to turn off protein-protein 
interactions.


I imagine it would be a huge memory hog and would run really slowly, but 
it's a possible solution.


-Justin


Mark

On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan  wrote:


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 
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

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Mark Abraham 
Hi,

Oh, I see. Yes that feature turns off both kinds of non-bonded
interactions. Then there is nothing useful for what you want.

Mark

On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan  wrote:

> 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 
> > 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  >
> > > > 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.
> > > > >
> > > >
> > > --
> > >

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Aram Davtyan 
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 
> 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 
> > > 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.
> >
>
>
> --
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Mark Abraham 
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  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 
> > 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.
>
-- 
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

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Aram Davtyan 
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 
> 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!
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>
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Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Mark Abraham 
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  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.
>
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