[gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 67
Mark Abraham
mark.j.abraham at gmail.com
Sat May 19 14:26:56 CEST 2018
Hi,
Please don't subscribe to a digest if you actually want to discuss. Nobody
will follow your replies.
You already need to know what oplsaa wants for its cutoffs, so you'd best
find that out from its literature before starting your work.
Mark
On Sat, May 19, 2018, 06:49 SHYANTANI MAITI <shyantani.maiti at gmail.com>
wrote:
> On 5/18/18 12:39 PM, SHYANTANI MAITI wrote:
> > Dear all,
> > What should be the value of d in editconf command for a protein-protein
> > complex of 500residues and length of protein is 6.5nm maximum.
> > I have simulated it using the command:
> > editconf -f conf.gro -bt cubic -d 6 -o box.gro
> > (considering 6 as the value of d).
> > I have considered the value of as 6 such that the cubic box is of
> > 12nm(d+d=6+6 from center of protein) length of each side, so that I can
> > give space to the protein-protein complex for creating its trajectory. Is
> > my concept correct?
> > I have also tried with the value of d as 1. When I am checking the
> > solvated.gro file for both d as 1and d as 6, I find that the protein is
> > solvated properly in both cases.
> > Can I consider the value of d as 1 instead of 6 for my specified
> > protein-protein complex?
>
> The solute-box buffer length depends on the force field (because of the
> required cutoffs) and has little to do with the protein itself. As long
> as you don't expect any large conformational changes or unfolding, then
> the typical approach is to set -d to the value of the longest cutoff
> required by your force field so you satisfy the minimum image
> convention. Then you have at least 2 cutoffs of buffer between images,
> which is a pretty safe approach to mitigate any potential water ordering
> effects if you try to shortcut things. This is not a hard and fast rule
> (and doubtless there will be people that would respond and argue about
> that approach), but it's a rule of thumb that you can apply and be
> pretty safe.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> Thank you for the reply.
> What should be the value of d if I consider OPLS-AA forcefield in my
> simulation?
>
> On Sat, May 19, 2018 at 5:25 AM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
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> >
> >
> > Today's Topics:
> >
> > 1. Re: Box size to be considered for a protein of length 500
> > residues and dimension of protein is 6.5nm maximum. (Justin Lemkul)
> > 2. Re: "energygrps" option for separating Bonded interactions
> > (Justin Lemkul)
> > 3. Re: "energygrps" option for separating Bonded interactions
> > (Debdas Dhabal)
> > 4. Re: "energygrps" option for separating Bonded interactions
> > (Debdas Dhabal)
> > 5. Re: "energygrps" option for separating Bonded interactions
> > (Justin Lemkul)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 18 May 2018 16:08:15 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Box size to be considered for a protein of
> > length 500 residues and dimension of protein is 6.5nm maximum.
> > Message-ID: <39041882-f197-2ce9-fffd-9f07cc0fb22e at vt.edu>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> >
> >
> > On 5/18/18 12:39 PM, SHYANTANI MAITI wrote:
> > > Dear all,
> > > What should be the value of d in editconf command for a protein-protein
> > > complex of 500residues and length of protein is 6.5nm maximum.
> > > I have simulated it using the command:
> > > editconf -f conf.gro -bt cubic -d 6 -o box.gro
> > > (considering 6 as the value of d).
> > > I have considered the value of as 6 such that the cubic box is of
> > > 12nm(d+d=6+6 from center of protein) length of each side, so that I can
> > > give space to the protein-protein complex for creating its trajectory.
> Is
> > > my concept correct?
> > > I have also tried with the value of d as 1. When I am checking the
> > > solvated.gro file for both d as 1and d as 6, I find that the protein is
> > > solvated properly in both cases.
> > > Can I consider the value of d as 1 instead of 6 for my specified
> > > protein-protein complex?
> >
> > The solute-box buffer length depends on the force field (because of the
> > required cutoffs) and has little to do with the protein itself. As long
> > as you don't expect any large conformational changes or unfolding, then
> > the typical approach is to set -d to the value of the longest cutoff
> > required by your force field so you satisfy the minimum image
> > convention. Then you have at least 2 cutoffs of buffer between images,
> > which is a pretty safe approach to mitigate any potential water ordering
> > effects if you try to shortcut things. This is not a hard and fast rule
> > (and doubtless there will be people that would respond and argue about
> > that approach), but it's a rule of thumb that y
> <https://maps.google.com/?q=pproach),+but+it's+a+rule+of+thumb+that+y&entry=gmail&source=g>ou
> can apply and be
> > pretty safe.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 18 May 2018 16:09:19 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] "energygrps" option for separating Bonded
> > interactions
> > Message-ID: <20c9fb67-3162-77a8-13db-5444d15867fd at vt.edu>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> >
> >
> > On 5/18/18 4:01 PM, Debdas Dhabal wrote:
> > > Dear all,
> > >
> > > I wonder if GROMACS has "energygrps" option (or any other similar
> > options)
> > > for bonded interactions (E_bond, E_ang, E_dih) for different groups.
> > Let's
> > > say I have three different chains in a single box and I want to extract
> > the
> > > bonded interactions for every chain separately. Would I be able to do
> > that
> > > on the fly during Gromacs run. I went through the webmanual and
> gmx_user
> > > page but didn't find any solution for that. I would be very grateful if
> > > someone could help me sharing how I could do this.
> >
> > energygrps will do nothing for bonded terms.
> >
> > If you want bonded energies of individual components, you will have to
> > strip out the coordinates you want from the trajectory (trjconv), make a
> > corresponding .tpr file (convert-tpr) and use md
> <https://maps.google.com/?q=onding+.tpr+file+(convert-tpr)+and+use+md&entry=gmail&source=g>run
> -rerun to compute
> > the potential energy of that species. Note that these quantities are
> > quite unlikely to have any physical meaning.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Fri, 18 May 2018 16:23:39 -0400
> > From: Debdas Dhabal <ddhabal at seas.upenn.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] "energygrps" option for separating Bonded
> > interactions
> > Message-ID:
> > <CALM0CUEiyQENg5rO9AJHE6NVYz+M6C0hbzOsB30ScnZ7OXorXw at mail.
> > gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Dear Justin,
> >
> > Thanks a lot for your kind help. Yes, these don't mean anything
> > quantitatively. I Just wanted to have a qualitative comparison between
> the
> > two states.
> >
> > With regards
> > Debdas
> >
> > On Fri, May 18, 2018 at 4:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 5/18/18 4:01 PM, Debdas Dhabal wrote:
> > >
> > >> Dear all,
> > >>
> > >> I wonder if GROMACS has "energygrps" option (or any other similar
> > options)
> > >> for bonded interactions (E_bond, E_ang, E_dih) for different groups.
> > Let's
> > >> say I have three different chains in a single box and I want to
> extract
> > >> the
> > >> bonded interactions for every chain separately. Would I be able to do
> > that
> > >> on the fly during Gromacs run. I went through the webmanual and
> gmx_user
> > >> page but didn't find any solution for that. I would be very grateful
> if
> > >> someone could help me sharing how I could do this.
> > >>
> > >
> > > energygrps will do nothing for bonded terms.
> > >
> > > If you want bonded energies of indiv
> <https://maps.google.com/?q=%0A%3E+%3E+If+you+want+bonded+energies+of+indiv&entry=gmail&source=g>idual
> components, you will have to
> > > strip out the coordinates you want from the trajectory (trjconv), make
> a
> > > corresponding .tpr file (convert-tpr) and use mdrun -rerun to compute
> the
> > > potential energy of that species. Note that these quantities are quite
> > > unlikely to have any physical meaning.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalemkul at 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-request at gromacs.org.
> > >
> >
> >
> >
> > --
> > Debdas Dhabal
> > Postdoctoral Researcher.
> > SEAS, Department of Chemical and Biomolecular Engineering,
> > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Fri, 18 May 2018 18:08:50 -0400
> > From: Debdas Dhabal <ddhabal at seas.upenn.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] "energygrps" option for separating Bonded
> > interactions
> > Message-ID:
> > <CALM0CUFRhgmMii8=6Qiat4nb-ApUmQWsg3HwNZ9bdsMP1+XAFg@
> > mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi Justin,
> >
> > When I follow the method you suggested I am getting an error.
> > (1) Using trjconv I have created a .trr file containing the coordinates
> of
> > the component for which I want to calculate the bonded energy.
> > (2) Now when I do *tpbconv_mpi -s topol.tpr (old tpr file) -f traj.trr
> > (containing component of my interest) -o tpxout.tpr *, it is showing an
> > error message -> "Number of atoms in Topology is not same as in
> > Trajectory".
> >
> > This means the trr file I am supplying should contain the trajectory of
> > whole system. If I do that then during *mdrun -s tpsout.tpr -rerun
> > traj.trr*,
> > it is giving energy for whole system not for that single component. It
> > would be very nice if you could kindly help me resolving this error.
> >
> > Thank you very much
> >
> > With regards
> >
> > On Fri, May 18, 2018 at 4:23 PM, Debdas Dhabal <ddhabal at seas.upenn.edu>
> > wrote:
> >
> > > Dear Justin,
> > >
> > > Thanks a lot for your kind help. Yes, these don't mean anything
> > > quantitatively. I Just wanted to have a qualitative comparison between
> > the
> > > two states.
> > >
> > > With regards
> > > Debdas
> > >
> > > On Fri, May 18, 2018 at 4:09 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >
> > >>
> > >>
> > >> On 5/18/18 4:01 PM, Debdas Dhabal wrote:
> > >>
> > >>> Dear all,
> > >>>
> > >>> I wonder if GROMACS has "energygrps" option (or any other similar
> > >>> options)
> > >>> for bonded interactions (E_bond, E_ang, E_dih) for different groups.
> > >>> Let's
> > >>> say I have three different chains in a single box and I want to
> extract
> > >>> the
> > >>> bonded interactions for every chain separately. Would I be able to do
> > >>> that
> > >>> on the fly during Gromacs run. I went through the webmanual and
> > gmx_user
> > >>> page but didn't find any solution for that. I would be very grateful
> if
> > >>> someone could help me sharing how I could do this.
> > >>>
> > >>
> > >> energygrps will do nothing for bonded terms.
> > >>
> > >> If you want bonded energies of individual components, you will have to
> > >> strip out the coordinates you want from the trajectory (trjconv),
> make a
> > >> corresponding .tpr file (convert-tpr) and use mdrun -rerun to compute
> > the
> > >> potential energy of that species. Note that these quantities are quite
> > >> unlikely to have any physical meaning.
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==================================================
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Assistant Professor
> > >> Virginia Tech Department of Biochemistry
> > >>
> > >> 303 Engel Hall
> > >> 340 West Campus Dr.
> > >> Blacksburg, VA 24061
> > >>
> > >> jalemkul at 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-request at gromacs.org.
> > >>
> > >
> > >
> > >
> > > --
> > > Debdas Dhabal
> > > Postdoctoral Researcher.
> > > SEAS, Department of Chemical and Biomolecular Engineering,
> > > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> > >
> >
> >
> >
> > --
> > Debdas Dhabal
> > Postdoctoral Researcher.
> > SEAS, Department of Chemical and Biomolecular Engineering,
> > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Fri, 18 May 2018 19:55:12 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] "energygrps" option for separating Bonded
> > interactions
> > Message-ID: <0c1886b8-13db-fe12-1a3b-c2ce5e962fcd at vt.edu>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> >
> >
> > On 5/18/18 6:08 PM, Debdas Dhabal wrote:
> > > Hi Justin,
> > >
> > > When I follow the method you suggested I am getting an error.
> > > (1) Using trjconv I have created a .trr file containi
> <https://maps.google.com/?q=jconv+I+have+created+a+.trr+file+containi&entry=gmail&source=g>ng
> the coordinates
> > of
> > > the component for which I want to calculate the bonded energy.
> > > (2) Now when I do *tpbconv_mpi -s topol.tpr (old tpr file) -f traj.trr
> > > (containing component of my interest) -o tpxout.tpr *, it is showing
> an
> > > error message -> "Number of atoms in Topology is not same as in
> > > Trajectory".
> > >
> > > This means the trr file I am supplying should contain the trajectory of
> > > whole system. If I do that then during *mdrun -s tpsout.tpr -rerun
> > traj.trr*,
> > > it is giving energy for whole system not for that single component. It
> > > would be very nice if you could kindly help me resolving this error.
> >
> > There is no need for a trajectory when creating a new .tpr file - that's
> > an antiquated method for extending simulations.
> >
> > All you need is:
> >
> > tpbconv -s old.tpr -o new.tpr (with a suitable selection that may or may
> > not require an index file)
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at 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-request at gromacs.org.
> >
> > End of gromacs.org_gmx-users Digest, Vol 169, Issue 67
> > ******************************************************
> >
>
>
>
> --
> Best regards,
> *Shyantani Maiti*
> --
> 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-request at gromacs.org.
>
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