[gmx-users] Tensor of inertia moments at each time step
Egidijus Kuprusevicius
ekuprusevicius at yahoo.com
Mon Nov 30 23:20:03 CET 2009
Hi,
Is it possible in GROMACS to extract from trajectory file 9 components of tensor of inertia moments at each time step? I know that it is possible to extract 3 vectors, but not whole tensor. Any suggestions?
Thank you
Egis
--- On Tue, 12/1/09, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org> wrote:
> From: gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
> Subject: gmx-users Digest, Vol 67, Issue 153
> To: gmx-users at gromacs.org
> Date: Tuesday, December 1, 2009, 12:43 AM
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> Today's Topics:
>
> 1. Re: Tabulated potentials make newbies
> crazy (Mark Abraham)
> 2. Re: Fwd: Last step before CG em.mdp
> (Francesco Pietra)
> 3. Re: Problem with output structures
> generated by energy
> minimization with GROMACS 4 (HAO
> JIANG)
> 4. Re: Fwd: Last step before CG em.mdp
> (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 01 Dec 2009 07:44:51 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Tabulated potentials make newbies
> crazy
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B142EC3.9010002 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> ms wrote:
> > Mark Abraham ha scritto:
> > > Sorry, I was a bit incomplete last night.
> Charge groups are the
> >> fundamental unit for neighbour-searching (3.4.2)
> to construct lists of
> >> charge groups for nonbonded interactions, which
> determine lists of
> >> atom-atom interactions. However, the nonbonded
> interactions are
> >> evaluated as nested sums, first over energy
> groups. So for energy groups
> >> of Protein and SOL, the neighbour search finds all
> pairs of charge
> >> groups that are both Protein and inside the
> cutoffs, and lists them.
> >> Then all Protein-SOL similarly, then all SOL-SOL.
> This requires that the
> >> energy groups be a union of only complete charge
> groups (and I am not
> >> aware that this is spelled out anywhere in the
> manual!). So for energy
> >> groups of Calpha, Rest_of_Protein and SOL, it
> would be necessary to use
> >> an individual charge group for each Calpha. This
> would usually mean it
> >> has a net non-integral charge that is equal in
> magnitude of the charge
> >> of the group from which it is taken. It is well
> known that small charge
> >> groups of non-integral charge can then wander back
> and forth across
> >> cut-off boundaries and generate artefacts.
> >
> > Ok, thanks for the clarification. This doesn't suggest
> a trivial
> > solution to the problem, quite the opposite: I
> understood correctly that
> > charge groups must be neutral, and this is impossible
> to do if we put
> > each C-alpha as a charge group.
> >
> > I can coarse the thing further -that's quite the plan,
> actually- and
> > eliminate electrostatics, but I hoped to have a look
> at what happens
> > with the new potential and getting it right, before
> going so far.
> >
> > So, even if the following:
> >>> The problem is that since I have a single
> molecule now, and the single
> >>> molecule must be neutral, so it must be all a
> single charge group
> >>> ("Therefore we have to keep groups of atoms
> with total charge 0
> >>> together. These groups are called charge
> groups.", 4.6.2).
> >
> > is not entirely correct, it is indeed correct that
> charge groups
> > *should* be neutral. Isn't it?
>
> Indeed. See 3.4.2 and ref therein.
>
> >> If you're running in single precision, that
> precision cannot represent
> >> values as large as 10^41. Since in any simulation
> (but particularly
> >> coarse-grained one) non-bonded atoms aren't going
> to get this close, the
> >> values are next to irrelevant. Just choose 10^38
> for anything larger
> >> than that.
> >
> > Right, it is probably precision problem. Thanks.
> >
> >>>>> Now, my questions are:
> >>>>> - What is the accepted range of values
> in tables?
> >>>> I don't think this is the problem.
> >>> It is the least problem probably, given my
> confusion on energy-charge
> >>> groups, but it seems it is too...
> >>>
> >>>>> - How do I define a steep repulsion
> potential correctly?
> >>>> It's terse, but manual 6.7 seems to have
> the necessary information.
> >>> 6.7 is one of the references I am obviously
> using, but it gives only
> >>> general (even if essential!!) information,
> nothing speficic on "good" or
> >>> "bad" potential shapes/values. But probably
> that's the least problem :)
> >> Knowing a sensible shape is your problem, if
> you're choosing to
> >> unbalance the force field by changing one of the
> contributing potentials...
> >
> > I meant "sensible" in the meaning of "can be
> interpolated more or less
> > faithfully / will be calculated with more or less
> artefacts" -of course
> > if it makes sense in the model is my problem...
>
> The cubic spline interpolation will do a mighty fine job of
> any function
> that is suitably continuous provided that the density of
> points is
> sufficiently fine... interpolating a sinusoid with a
> density comparable
> with the period would obviously be a disaster!
>
> Mark
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 30 Nov 2009 21:49:13 +0100
> From: Francesco Pietra <francesco.pietra at accademialucchese.it>
> Subject: Re: [gmx-users] Fwd: Last step before CG em.mdp
> To: jalemkul at vt.edu,
> Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <b87c422a0911301249k5b58ce26tf7b35b7f2e651dc9 at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul <jalemkul at vt.edu>
> wrote:
> >
> >
> > Francesco Pietra wrote:
> >>
> >> Failed to specify that both the DPPC bilayer and
> the box of water are
> >> from equilibrated systems in MARTIN web, while the
> protein was Amber
> >> minimized (and MD) before generating the CG.
> >>
> >> I have tried the cg protein alone
> >>
> >> genbox -cp my.pdb -box 15 -o my.gro
> >>
> >
> > Again I ask why you are using SPC as the solvent. If
> you indeed want to use
> > the MARTINI CG water representation, you must pass its
> configuration
> > explicitly to the -cs flag. Otherwise, the default
> (spc216.gro) is used.
>
> The water that I set around the extracellular part of the
> protein was
> equilibrated cg water (by just multiplying the box
> furnished on
> MARTINI). In relation to the command above, I don't
> understand your
> remark, simply because there is no water at all, both in
> the input
> .pdb and output.gro. This is true for my previous post,
> too.
>
>
> >
> > Are you defining the protein's position in the box
> before solvation? Using
> > editconf -c is your friend.
>
> I did present work before getting your mail. Curiously,
> gmail now
> places your mail in spam. Luckily I noticed that.
> A point I have to pay much attention to - for a possible
> major mistake
> in my procedure - is your "before solvation". I assumed no
> solvation
> at all.
>
>
>
> >
> >> grompp -f em.mdp -c my.gro -p my.top -o topol.tpr
> >>
> >> mdrun -v -s topol.tpr
> >>
> >> steepest descents converged to machine precision
> but not to the
> >> requested Fmax < 2000
> >>
> >> Pot Ener 7.1e+08
> >> Max force 6.1e+10 on atom 983
> >> Norm of force 2.5e+11
> >>
> >> confout.gro shows that one of the subunits has
> been displaced from the
> >> multimer (apparently both intact) There is a long
> bond between the
> >> displaced subunit and the rest of the multimer,
> very closely to the
> >> atom 983 of max force, located in the pore region.
> I have scarce
> >> experience with gromacs yet, hope that this
> suggests remedies. I used
> >> a crude version of em.mdp.
> >>
> >
> > Well, there are several potential problems. One is
> the box size (as I
> > mentioned in my last message). The other question is
> whether or not the
> > conversion from atomistic to CG was done correctly.
> I know I have mentioned
> > the problems with the MARTINI script a number of
> times, and perhaps this has
> > also come up in our discussions before, but do check
> that the starting CG
> > coordinates make sense.
>
> The cg protein model superimposes nicely to the full-atom
> model. The
> dimensions I gave in my previous mail were DPPC and W
> inclusive but
> "-box 15" is still to small. The protein might have seen
> its neighbor.
>
> >
> > Beyond that, try an in vacuo minimization of your
> protein and see what
> > happens there.
>
> Do you mean without setting "-box"? I got confused about
> that, I
> thought to have vacum around the protein (or the
> protein+DPPC+W of
> previous mail) with
>
> genbox -cp my.pdb -box 15 -o my.gro
>
>
> I'll try tomorrow to implement all your suggestions. Thanks
> a lot
> francesco
>
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list.
> Use the www interface
> > or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 30 Nov 2009 15:50:48 -0500
> From: "HAO JIANG" <hj.public at gmail.com>
> Subject: Re: [gmx-users] Problem with output structures
> generated by
> energy minimization
> with GROMACS 4
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <3774C6B488994877B47FA3D7F3F59D2A at leihao>
> Content-Type: text/plain;
> charset="UTF-8"
>
> Tsjerk,
>
> Thanks for your reply.
>
> I am doing a simple test case with 500 SPC/E water
> molecules. First I did minimization with steepest decent,
> using a command like
>
> mdrun -pd -s water.gro.tpr -c final.gro
>
> The generated md.log looks like the following:
> ----------------
> Step
> Time
> Lambda
> 0
> 0.00000
> 0.00000
> Energies (kJ/mol)
> LJ (SR) Disper.
> corr. Coulomb (SR) Coul.
> recip. Potential
>
> 4.70442e+03 -7.34875e+02 -2.65916e+04 -1.28439e+03 -2.39065e+04
> Pressure (bar)
> 2.27899e+04
> .
> .
> .
> Step
> Time
> Lambda
> 1000
> 1000.00000
> 0.00000
> Energies (kJ/mol)
> LJ (SR) Disper.
> corr. Coulomb (SR) Coul.
> recip. Potential
>
> 5.53526e+03 -7.34875e+02 -3.22651e+04 -1.33018e+03 -2.87949e+04
> Pressure (bar)
> 2.42765e+04
>
>
> Steepest Descents did not converge to Fmax < 1 in 1001
> steps.
> Potential Energy = -2.87949018657418e+04
> Maximum force =
> 6.95206177080918e+01 on atom 1033
> Norm of force =
> 3.71165837023948e+00
> --------
>
> Just for testing I tried to do further optimization. I
> created a new tpr with the generated final.gro file and the
> old top and mdp files, then run mdrun again.
>
> This time the generated md.log looks like the following:
>
> ===
> Step
> Time
> Lambda
> 0
> 0.00000
> 0.00000
> Energies (kJ/mol)
> LJ (SR) Disper.
> corr. Coulomb (SR) Coul.
> recip. Potential
>
> 4.70442e+03 -7.34875e+02 -2.65916e+04 -1.28439e+03 -2.39065e+04
> Pressure (bar)
> 2.27899e+04
>
> .
> .
> .
> ====
>
> So it seems like final.gro has a potential energy that is
> very close to that of the original, un-optimized
> structure.
>
> While I repeat the same procedure with Gromacs 3.3,
> everything works as expected. For the first optimization I
> got
>
> ---
> Step
> Time
> Lambda
> 0
> 0.00000
> 0.00000
> Energies (kJ/mol)
> LJ (SR) Disper.
> corr. Coulomb (SR) Coul.
> recip. Potential
>
> 4.70486e+03 -7.34875e+02 -2.65916e+04 -1.28441e+03 -2.39060e+04
> Kinetic En. Total
> Energy Temperature Pressure (bar)
> 0.00000e+00 0.00000e+00
> 0.00000e+00 -1.63608e+03
> .
> .
> .
> Step
> Time
> Lambda
> 999
> 999.00000 0.00000
>
> Energies (kJ/mol)
> LJ (SR) Disper.
> corr. Coulomb (SR) Coul.
> recip. Potential
>
> 5.48610e+03 -7.34875e+02 -3.21894e+04 -1.29343e+03 -2.87316e+04
> Kinetic En. Total
> Energy Temperature Pressure (bar)
> 0.00000e+00 0.00000e+00
> 0.00000e+00 -1.63608e+06
>
> Step
> Time
> Lambda
> 1000
> 1000.00000
> 0.00000
>
>
> Steepest Descents did not converge to Fmax < 1 in 1001
> steps.
> Potential Energy = -2.87316123776041e+04
> Maximum force =
> 2.72102300902620e+01 on atom 136
> Norm of force =
> 2.08471187918543e+02
> ---
>
> and for the further optimization I got
>
> ===
> Step
> Time
> Lambda
> 0
> 0.00000
> 0.00000
> Energies (kJ/mol)
> LJ (SR) Disper.
> corr. Coulomb (SR) Coul.
> recip. Potential
>
> 5.48626e+03 -7.34875e+02 -3.21871e+04 -1.29320e+03 -2.87289e+04
> Kinetic En. Total
> Energy Temperature Pressure (bar)
> 0.00000e+00 0.00000e+00
> 0.00000e+00 -1.63608e+03
> .
> .
> .
> ===
>
> I don't know what causes the difference.
>
> Hao Jiang
>
>
>
>
> ----- Original Message -----
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: 2009年11月30日 12:37 PM
> Subject: Re: [gmx-users] Problem with output structures
> generated by energy minimization with GROMACS 4
>
>
> Ni Hao,
>
> You don't give too much information here. What exactly are
> you doing?
> What are the commands? What's the difference between the
> first and the
> second pass of EM? One thing to check is whether the
> output/input file
> has a correct box definition.
>
> Cheers,
>
> Tsjerk
>
> 2009/11/30 HAO JIANG <hj.public at gmail.com>:
> > Hi,
> >
> > I got a problem with the output structure files
> (gro/trr/xtc) generated by
> > the energy minimization with GROMACS 4. That is, when
> I used the generated
> > structure as the input for further minimizations or MD
> simulations, I got
> > very large potential energy and forces at step 0, as
> if the structure had
> > not been optimized at all. On the other hand, there is
> no problem when
> > the input structure is taken from a previous MD run,
> and I got the expected
> > potential at step 0. There is no problem, too, if I
> use GROMACS 3 to do the
> > minimization.
> >
> > Any help is greatly appreciated!
> >
> > Hao Jiang
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list.
> Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use
> the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> ------------------------------
>
> Message: 4
> Date: Mon, 30 Nov 2009 16:43:22 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Fwd: Last step before CG em.mdp
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <4B143C7A.3060303 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> Francesco Pietra wrote:
> > On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul
> <jalemkul at vt.edu>
> wrote:
> >>
> >> Francesco Pietra wrote:
> >>> Failed to specify that both the DPPC bilayer
> and the box of water are
> >>> from equilibrated systems in MARTIN web, while
> the protein was Amber
> >>> minimized (and MD) before generating the CG.
> >>>
> >>> I have tried the cg protein alone
> >>>
> >>> genbox -cp my.pdb -box 15 -o my.gro
> >>>
> >> Again I ask why you are using SPC as the
> solvent. If you indeed want to use
> >> the MARTINI CG water representation, you must pass
> its configuration
> >> explicitly to the -cs flag. Otherwise, the
> default (spc216.gro) is used.
> >
> > The water that I set around the extracellular part of
> the protein was
> > equilibrated cg water (by just multiplying the box
> furnished on
> > MARTINI). In relation to the command above, I don't
> understand your
> > remark, simply because there is no water at all, both
> in the input
> > .pdb and output.gro. This is true for my previous
> post, too.
> >
>
> Oops, my mistake. I forgot that -cs was optional, and
> not taken as default :)
> Never mind that comment.
>
> >
> >> Are you defining the protein's position in the box
> before solvation? Using
> >> editconf -c is your friend.
> >
> > I did present work before getting your mail.
> Curiously, gmail now
> > places your mail in spam. Luckily I noticed that.
> > A point I have to pay much attention to - for a
> possible major mistake
> > in my procedure - is your "before solvation". I
> assumed no solvation
> > at all.
> >
> >
> >
> >>> grompp -f em.mdp -c my.gro -p my.top -o
> topol.tpr
> >>>
> >>> mdrun -v -s topol.tpr
> >>>
> >>> steepest descents converged to machine
> precision but not to the
> >>> requested Fmax < 2000
> >>>
> >>> Pot Ener 7.1e+08
> >>> Max force 6.1e+10 on atom 983
> >>> Norm of force 2.5e+11
> >>>
> >>> confout.gro shows that one of the subunits has
> been displaced from the
> >>> multimer (apparently both intact) There is a
> long bond between the
> >>> displaced subunit and the rest of the
> multimer, very closely to the
> >>> atom 983 of max force, located in the pore
> region. I have scarce
> >>> experience with gromacs yet, hope that this
> suggests remedies. I used
> >>> a crude version of em.mdp.
> >>>
> >> Well, there are several potential problems.
> One is the box size (as I
> >> mentioned in my last message). The other
> question is whether or not the
> >> conversion from atomistic to CG was done
> correctly. I know I have mentioned
> >> the problems with the MARTINI script a number of
> times, and perhaps this has
> >> also come up in our discussions before, but do
> check that the starting CG
> >> coordinates make sense.
> >
> > The cg protein model superimposes nicely to the
> full-atom model. The
> > dimensions I gave in my previous mail were DPPC and W
> inclusive but
> > "-box 15" is still to small. The protein might have
> seen its neighbor.
> >
>
> Then that's certainly the first problem to fix. This
> is why I generally use
> editconf for defining the box (and why I keep recommending
> it). For a simple
> protein in water, using a command like:
>
> editconf -c -d 1.0
>
> will define a suitably-sized box so that you don't have to
> guess at the box
> dimensions. There is no such option with genbox.
>
> >> Beyond that, try an in vacuo minimization of your
> protein and see what
> >> happens there.
> >
> > Do you mean without setting "-box"? I got confused
> about that, I
> > thought to have vacum around the protein (or the
> protein+DPPC+W of
> > previous mail) with
> >
>
> You can disregard that comment, I had assumed from reading
> the earlier post that
> you had solvated the structure. If the protein does
> not minimize by itself
> (hence, in vacuo) then perhaps your issue comes from your
> box dimensions. Seems
> most likely at this point.
>
> I don't think you want a vacuum around your system.
> That's the whole point of
> PBC is it not - to avoid boundary conditions and "droplet"
> formation? What you
> want to do is assign a box that actually fits your system
> :)
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 67, Issue 153
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