[gmx-users] gromacs.org_gmx-users Digest, Vol 124, Issue 58
Nikolaos Michelarakis
nm884 at york.ac.uk
Tue Aug 12 19:57:21 CEST 2014
Thank you very much for your answer!
this is the link to the whole forcefield directory:
https://drive.google.com/folderview?id=0Bxa-J2wEpEeqbnZDVmpmQ0JGcUE&usp=sharing
Since it's my first time doing something like that, i might have done
something wrong in adding the iron in the forcefield. Since iron was
already present in the heme group of the forcefield i used FE3+ as a name.
please let me know if I have done something wrong.
I tried playing around with the charge of the iron, changed it to 0.4, and
these are the new files i got for every step, along with the topology. This
time the force on the whole structure was larger and a lot smaller on the
oxygen bound on the iron:
https://drive.google.com/folderview?id=0Bxa-J2wEpEeqME82TjhJUnQ0TzQ&usp=sharing
I would appreciate it If you could take a look at the forcefield and let me
know if everything is correct in there and I will try finding the correct
parameters.
Thank you again for all your help.
Nicholas
On 12 August 2014 18:35, <gromacs.org_gmx-users-request at maillist.sys.kth.se>
wrote:
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> Today's Topics:
>
> 1. Setting Non-bonded Scaling Constant for Amber FF (Johnny Lu)
> 2. Re: Setting Non-bonded Scaling Constant for Amber FF
> (Justin Lemkul)
> 3. Re: Iron containing structure simulation crash
> (Nikolaos Michelarakis)
> 4. Re: Iron containing structure simulation crash
> (Nikolaos Michelarakis)
> 5. Re: Iron containing structure simulation crash (Justin Lemkul)
> 6. Re: potential energy (Meenakshi Rajput)
> 7. Re: Polymer not diffusing into membrane (Alex s)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 12 Aug 2014 11:57:45 -0400
> From: Johnny Lu <johnny.lu128 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Setting Non-bonded Scaling Constant for Amber FF
> Message-ID:
> <CACFK4+NF-YOP3tJ6TZZKm9zJhRob1Wv-87ZB=
> nf50Rqnq5B7LQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi.
>
> I'm a first year PhD student, and wonder if we have to set the equivalent
> of scnb and scee (1-4 nonbond scaling facor for vdw and for electrostatic)
> in the gromacs mdp file when we use the Amber99SB force field in gromacs?
>
> Thank you in advance.
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 12 Aug 2014 12:00:04 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Setting Non-bonded Scaling Constant for Amber
> FF
> Message-ID: <53EA3A04.1040906 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 8/12/14, 11:57 AM, Johnny Lu wrote:
> > Hi.
> >
> > I'm a first year PhD student, and wonder if we have to set the equivalent
> > of scnb and scee (1-4 nonbond scaling facor for vdw and for
> electrostatic)
> > in the gromacs mdp file when we use the Amber99SB force field in gromacs?
> >
>
> You don't. These values are specified in the [defaults] directive in
> forcefield.itp.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 12 Aug 2014 17:20:31 +0100
> From: Nikolaos Michelarakis <nm884 at york.ac.uk>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Iron containing structure simulation crash
> Message-ID:
> <CADp34cnycCQxS7gbU3WzL5Jf8L7aRhj=
> EDGR5XQg591DCo343A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> >An output coordinate file is always produced unless mdrun completely fails
> and
> >seg faults. That doesn't mean the coordinates are sane. It's meant to
> help you
> >diagnose in cases like this where you have an absurd force on some atom.
>
> >What is atom 2832? What's around it? Is there anything obviously
> clashing with
> >it? Also check the topology for errors.
>
> >-Justin
>
> The atom is the iron that I introduced. It is bound to an oxygen which is
> itself bound to the carbon of a ring. It is found on the spot where the
> ligand, not introduced in the simulation yet, is binding to the protein.
> There are a few carbons and nitrogens but nothing in close proximity or
> clashing with it.
> The topology seems ok to me. This is the link to the file, the iron shows a
> charge of +3, could this be the cause of such a great force?
>
>
> https://drive.google.com/file/d/0Bxa-J2wEpEeqTC1UX2tNOG1LVms/edit?usp=sharing
>
> Thank you again,
>
> Nicholas
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 12 Aug 2014 17:20:31 +0100
> From: Nikolaos Michelarakis <nm884 at york.ac.uk>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Iron containing structure simulation crash
> Message-ID:
> <CADp34cnycCQxS7gbU3WzL5Jf8L7aRhj=
> EDGR5XQg591DCo343A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> >An output coordinate file is always produced unless mdrun completely fails
> and
> >seg faults. That doesn't mean the coordinates are sane. It's meant to
> help you
> >diagnose in cases like this where you have an absurd force on some atom.
>
> >What is atom 2832? What's around it? Is there anything obviously
> clashing with
> >it? Also check the topology for errors.
>
> >-Justin
>
> The atom is the iron that I introduced. It is bound to an oxygen which is
> itself bound to the carbon of a ring. It is found on the spot where the
> ligand, not introduced in the simulation yet, is binding to the protein.
> There are a few carbons and nitrogens but nothing in close proximity or
> clashing with it.
> The topology seems ok to me. This is the link to the file, the iron shows a
> charge of +3, could this be the cause of such a great force?
>
>
> https://drive.google.com/file/d/0Bxa-J2wEpEeqTC1UX2tNOG1LVms/edit?usp=sharing
>
> Thank you again,
>
> Nicholas
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 12 Aug 2014 12:36:01 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Iron containing structure simulation crash
> Message-ID: <53EA4271.1040006 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 8/12/14, 12:20 PM, Nikolaos Michelarakis wrote:
> >> An output coordinate file is always produced unless mdrun completely
> fails
> > and
> >> seg faults. That doesn't mean the coordinates are sane. It's meant to
> > help you
> >> diagnose in cases like this where you have an absurd force on some atom.
> >
> >> What is atom 2832? What's around it? Is there anything obviously
> > clashing with
> >> it? Also check the topology for errors.
> >
> >> -Justin
> >
> > The atom is the iron that I introduced. It is bound to an oxygen which is
> > itself bound to the carbon of a ring. It is found on the spot where the
> > ligand, not introduced in the simulation yet, is binding to the protein.
> > There are a few carbons and nitrogens but nothing in close proximity or
> > clashing with it.
> > The topology seems ok to me. This is the link to the file, the iron
> shows a
> > charge of +3, could this be the cause of such a great force?
> >
>
> Given that that's a really unphysical situation, it's certainly a
> contributing
> factor. As I'm sure I've said before, additive models fail spectacularly
> for
> metals like these. That is a massive charge density, when in reality, the
> charge is spread over the ligating molecules. You'll probably have to do
> some
> real parametrization to develop suitable charges and LJ terms, rather than
> relying on whatever there might already be.
>
> >
> https://drive.google.com/file/d/0Bxa-J2wEpEeqTC1UX2tNOG1LVms/edit?usp=sharing
> >
>
> In isolation, the topology doesn't help much. A full force field
> directory and
> the coordinate file would illuminate any obvious errors.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 12 Aug 2014 10:03:52 -0700
> From: Meenakshi Rajput <ashi.rajput39 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] potential energy
> Message-ID:
> <CAH5GTB+1ZYT=vNbSE6Q=
> vwG3J1vFDgu5s001YKBEhj4tcdiuQw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thanks a lot Justin.
> On Aug 11, 2014 10:36 PM, "Meenakshi Rajput" <ashi.rajput39 at gmail.com>
> wrote:
>
> > thanks...can you help me out with the mdp file settings with charmm force
> > field(proteins)? I am a new user to gromacs and stuck here.
> >
> >
> > On Mon, Aug 11, 2014 at 5:07 AM, Meenakshi Rajput <
> ashi.rajput39 at gmail.com
> > > wrote:
> >
> >> Thanks..but if potential becomes positive after energy minimisation run,
> >> then is it normal or there is some prblm with my mdp file. I used the
> same
> >> mdp file for this run also. I used charmm force field.
> >> On Aug 11, 2014 2:32 PM, "Meenakshi Rajput" <ashi.rajput39 at gmail.com>
> >> wrote:
> >>
> >>> hi users
> >>> i have run energy minimisation of docked complex by using this
> min.mdp:-
> >>>
> >>> cpp = /lib/cpp ; Preprocessor
> >>> include = -I../top ; Directories to include in the topology
> >>> format
> >>> integrator = steep
> >>> emtol = 1000 ; Stop minimization when the energy changes
> >>> by less than emtol kJ/mol.
> >>> nsteps = 200 ; Maximum number of (minimization) steps to
> >>> perform
> >>> nstenergy = 10 ; Write energies to disk every nstenergy steps
> >>> nstxtcout = 10 ; Write coordinates to disk every nstxtcout
> >>> steps
> >>> xtc_grps = Protein ; Which coordinate group(s) to write to disk
> >>> energygrps = Protein ; Which energy group(s) to write to disk
> >>> nstlist = 5 ; Frequency to update the neighbor list and
> >>> long range forces
> >>> ns_type = grid ; Method to determine neighbor list (simple,
> >>> grid)
> >>> rlist = 1.2 ; Cut-off for making neighbor list (short
> >>> range forces)
> >>> coulombtype = PME ; Treatment of long range electrostatic
> >>> interactions
> >>> rcoulomb = 1.2 ; long range electrostatic cut-off
> >>> rvdw = 1.2 ; long range Van der Waals cut-off
> >>> constraints = none ; Bond types to replace by constraints
> >>> pbc = xyz ; Periodic Boundary Conditions (yes/no0
> >>> After the run, potential energy is negative. can you tell me whats the
> >>> problem??
> >>>
> >>
> >
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 12 Aug 2014 18:35:35 +0100
> From: Alex s <as1783 at hotmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Polymer not diffusing into membrane
> Message-ID: <BAY181-W3519935BCE20C8AA29F138D0EA0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I've run it for 200 ns which I think is long enough allow the polymer to
> diffuse.
>
> > Date: Tue, 12 Aug 2014 10:41:52 +0200
> > From: devicerandom at gmail.com
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Polymer not diffusing into membrane
> >
> > How long is your simulation? Are you sure it is long enough to see what
> you
> > want to see?
> > On 12 Aug 2014 07:15, "Alex s" <as1783 at hotmail.com> wrote:
> >
> > > Dear Gromacs users
> > > I'm not sure if this a question suitable for this forum but I would
> > > greatly appreciate it if you can help me in anyway regarding this
> issue.
> > > I've have a system made up of a lipid bilayer, water and a single chain
> > > polymer. My aim is to place the polymer just above the lipid bilayer
> in
> > > the water phase and let it diffuse into the bilayer. This polymer has
> been
> > > shown to interact with the lipid bilayer in previous studies us. The
> issue
> > > I'm having is that in my simulation the polymer stays in the water
> phase
> > > just hovering above the lipid membrane and never interacts or diffuses.
> > > I've tried simulating it in a number of different ways by varying the
> > > number of water molecules, changing box size or polymer position
> however I
> > > haven't had any success yet. The main steps in setting up my system is
> as
> > > follows:
> > > 1. Simulate the Lipid bilayer alone to equilibrate it. 2. Take the
> final
> > > box size of the lipid bilayer and use it to place the Polymer at
> specific
> > > point just above the lipid bilayer. 3. Perform energy minimization on
> the
> > > system4. Perform NVT and NPT5. Run the simulation
> > > Any advice would be helpful
> > > Regards
> > > Alex
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
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> > > posting!
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> > >
> > --
> > Gromacs Users mailing list
> >
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