[gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul)
Collins Nganou
nganoucollins at gmail.com
Thu Aug 1 22:55:37 CEST 2013
Dear Justin,
Thanks....
I am simulating a DNA with different residues. I am looking the way to
extract only the energy of adjacent DT. I intend print out this energy
group via the energygrps = DT
I would like to have only DT in the index file. But it doesn't work.
This is the error encounter:
Fatal error:
Group DNA referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Best regards
Collins
On Thu, Aug 1, 2013 at 1:16 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: Interaction energy between specific residue in a set of
> residues (Justin Lemkul)
> 2. Re: inconsistent energy drops (Brad Van Oosten)
> 3. Re: Expanded ensemble simulation died with fatal error:
> Something wrong in choosing new lambda state with a Gibbs move
> (Michael Shirts)
> 4. fatal error with charmm/amber forcefield (Sanku M)
> 5. Re: Re: inconsistent energy drops (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 31 Jul 2013 16:27:52 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Interaction energy between specific residue
> in a set of residues
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51F97348.1010406 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 7/31/13 4:20 PM, Collins Nganou wrote:
> > Dear all,
> >
> > I am looking how I can extract the interaction energy between specific
> > residue in a set of residues.
> >
>
> Nonbonded energy terms are decomposed using energygrps in the .mdp file
> along
> with suitable index groups.
>
> > example:
> >
> > I have DT and DA residues, I would like to plot only the energy of the
> DT.
> > I can extract the DT with the index file, But I am missing information on
> > how to plot the energy base on my index file where I can select only DT.
> >
>
> You can create index groups for any base or bases you want individually.
> You
> haven't shown us what you've done, so it's hard to critique beyond that.
>
> > I was only looking the way to extract the c5-c6 distance of adjacent DT
> > without include DA.
> >
>
> Distances are calculated with g_dist and suitable index groups.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 31 Jul 2013 13:45:02 -0700 (PDT)
> From: Brad Van Oosten <bv07ay at brocku.ca>
> Subject: [gmx-users] Re: inconsistent energy drops
> To: gmx-users at gromacs.org
> Message-ID: <1375303502523-5010267.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> looking at the first 2 peaks, they are created from single outlying points
> in
> the trajectory. Visually, I can see no discernible difference between it
> and
> the frame before/after with the higher energy.
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/inconsistent-energy-drops-tp5010260p5010267.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 31 Jul 2013 17:17:04 -0400
> From: Michael Shirts <mrshirts at gmail.com>
> Subject: Re: [gmx-users] Expanded ensemble simulation died with fatal
> error: Something wrong in choosing new lambda state with a Gibbs
> move
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CA+zJb=gQY5BdJ_L9P_+nAnQhiWGe0nR+xEqZ7Pvf-UWiEq-H=
> g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Dejun-
>
> The basic problem is that for this particular configuration, the
> current state is the only state with nonzero weight. Note that the
> state with the second highest weight has weight 10^-7. When it tries
> to compare weights in single precision, it has a numerical overflow
> and fails.
>
> A few things:
>
> 1. This really should be more robust, so that it will realize it's
> supposed to stay in the most likely state, since that's the only state
> with nonzero weight. I have a fix that I've been working on for
> exactly this problem, but it's not quite ready yet. Hopefully in the
> next couple of days.
>
> 2. This problem is very unlikely to occur in double precision, if you
> can afford the performance hit in the meantime.
>
> 3. If this is a typical average difference, exchanges will be very
> unlikely. You should probably choose your lambda intervals to be a
> bit closer together at the end range.
>
> Hopefully this will give you enough information to move forward for
> the time being until a better fix is implemented.
>
>
> On Wed, Jul 31, 2013 at 2:15 PM, Dejun Lin <dejun.lin at gmail.com> wrote:
> > Hi all,
> >
> > I'm running an expanded ensemble simulation using gromacs 4.6.3 and it
> > crashed with the error:
> >
> > Fatal error:
> > Something wrong in choosing new lambda state with a Gibbs move --
> probably
> > underflow in weight determination.
> > Denominator is: 0 1.0000002384e+00
> > i dE numerator weights
> > 0 -9.1451739502e+02 0.0000000000e+00 0.0000000000e+00
> > 1 -9.0000128174e+02 0.0000000000e+00 0.0000000000e+00
> > 2 -8.8548516846e+02 0.0000000000e+00 0.0000000000e+00
> > 3 -8.7096899414e+02 0.0000000000e+00 0.0000000000e+00
> > 4 -8.5645288086e+02 0.0000000000e+00 0.0000000000e+00
> > 5 -8.4193676758e+02 0.0000000000e+00 0.0000000000e+00
> > 6 -8.2742059326e+02 0.0000000000e+00 0.0000000000e+00
> > 7 -8.1290447998e+02 0.0000000000e+00 0.0000000000e+00
> > 8 -7.9838836670e+02 0.0000000000e+00 0.0000000000e+00
> > 9 -7.8387219238e+02 0.0000000000e+00 0.0000000000e+00
> > 10 -7.6935607910e+02 0.0000000000e+00 0.0000000000e+00
> > 11 -7.5483990479e+02 0.0000000000e+00 0.0000000000e+00
> > 12 -7.4032379150e+02 0.0000000000e+00 0.0000000000e+00
> > 13 -7.2580767822e+02 0.0000000000e+00 0.0000000000e+00
> > 14 -7.1129150391e+02 0.0000000000e+00 0.0000000000e+00
> > 15 -6.9677539062e+02 0.0000000000e+00 0.0000000000e+00
> > 16 -6.8225927734e+02 0.0000000000e+00 0.0000000000e+00
> > 17 -6.6774316406e+02 0.0000000000e+00 0.0000000000e+00
> > 18 -6.5322698975e+02 0.0000000000e+00 0.0000000000e+00
> > 19 -6.3871087646e+02 0.0000000000e+00 0.0000000000e+00
> > 20 -6.2419470215e+02 0.0000000000e+00 0.0000000000e+00
> > 21 -6.0967858887e+02 0.0000000000e+00 0.0000000000e+00
> > 22 -5.9516247559e+02 0.0000000000e+00 0.0000000000e+00
> > 23 -5.8064630127e+02 0.0000000000e+00 0.0000000000e+00
> > 24 -5.6613018799e+02 0.0000000000e+00 0.0000000000e+00
> > 25 -5.5161407471e+02 0.0000000000e+00 0.0000000000e+00
> > 26 -5.3709790039e+02 0.0000000000e+00 0.0000000000e+00
> > 27 -5.2258178711e+02 0.0000000000e+00 0.0000000000e+00
> > 28 -5.0806564331e+02 0.0000000000e+00 0.0000000000e+00
> > 29 -4.9354953003e+02 0.0000000000e+00 0.0000000000e+00
> > 30 -4.7903335571e+02 0.0000000000e+00 0.0000000000e+00
> > 31 -4.6451724243e+02 0.0000000000e+00 0.0000000000e+00
> > 32 -4.5000018311e+02 0.0000000000e+00 0.0000000000e+00
> > 33 -4.3548400879e+02 0.0000000000e+00 0.0000000000e+00
> > 34 -4.2096792603e+02 0.0000000000e+00 0.0000000000e+00
> > 35 -4.0645178223e+02 0.0000000000e+00 0.0000000000e+00
> > 36 -3.9193563843e+02 0.0000000000e+00 0.0000000000e+00
> > 37 -3.8107025146e+02 0.0000000000e+00 0.0000000000e+00
> > 38 -3.6290338135e+02 0.0000000000e+00 0.0000000000e+00
> > 39 -3.4838723755e+02 0.0000000000e+00 0.0000000000e+00
> > 40 -3.3387109375e+02 0.0000000000e+00 0.0000000000e+00
> > 41 -3.1935494995e+02 0.0000000000e+00 0.0000000000e+00
> > 42 -3.0483883667e+02 0.0000000000e+00 0.0000000000e+00
> > 43 -2.9032269287e+02 0.0000000000e+00 0.0000000000e+00
> > 44 -2.7580654907e+02 0.0000000000e+00 0.0000000000e+00
> > 45 -2.6129040527e+02 0.0000000000e+00 0.0000000000e+00
> > 46 -2.4677430725e+02 0.0000000000e+00 0.0000000000e+00
> > 47 -2.3225816345e+02 0.0000000000e+00 0.0000000000e+00
> > 48 -2.1774200439e+02 0.0000000000e+00 0.0000000000e+00
> > 49 -2.0322586060e+02 0.0000000000e+00 0.0000000000e+00
> > 50 -1.8970976257e+02 0.0000000000e+00-1.0000000000e+00
> > 51 -1.7419361877e+02 0.0000000000e+00 0.0000000000e+00
> > 52 -1.5967747498e+02 0.0000000000e+00 0.0000000000e+00
> > 53 -1.4516131592e+02 0.0000000000e+00 0.0000000000e+00
> > 54 -1.3064523315e+02 0.0000000000e+00 0.0000000000e+00
> > 55 -1.1612908173e+02 0.0000000000e+00 0.0000000000e+00
> > 56 -1.0161293030e+02 7.0064923216e-45 0.0000000000e+00
> > 57 -8.7096786499e+01 1.4939846888e-38 0.0000000000e+00
> > 58 -7.2580688477e+01 3.0102835162e-32 0.0000000000e+00
> > 59 -5.8064540863e+01 6.0658294505e-26 0.0000000000e+00
> > 60 -4.3548393250e+01 1.2222865341e-19 0.0000000000e+00
> > 61 -2.9032243729e+01 2.4629560544e-13 0.0000000000e+00
> > 62 -1.5516148567e+01 1.8256696421e-07-1.0000000000e+00
> > 63 0.0000000000e+00 9.9999976158e-01-1.0000000000e+00
> >
> > The mdp options for the free energy and expanded ensemble stuff are:
> >
> > free-energy = expanded
> >
> > ; no need to mess with these for now
> > ;--------
> > sc-alpha = 0
> > sc-power = 0
> > sc-r-power = 6
> > sc-coul = no
> > -------
> >
> > ; Which intermediate state are we simulating?
> > -------
> > init-lambda-state = 0
> >
> > ; What are the values of lambda at the intermediate states?
> > ;-------
> > ; fep-lambdas = 0.0 0.06667 0.1333 0.2 0.2667 0.3333 0.4
> 0.4667
> > 0.5333 0.6 0.6667 0.7333 0.8 0.8667 0.9333 1.0
> > bonded-lambdas = 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000
> > vdw-lambdas = 0.000000 0.015873 0.031746 0.047619 0.063492
> > 0.079365 0.095238 0.111111 0.126984 0.142857 0.158730 0.174603 0.190476
> > 0.206349 0.222222 0.238095 0.253968 0.269841 0.285714 0.301587 0.317460
> > 0.333333 0.349206 0.365079 0.380952 0.396825 0.412698 0.428571 0.444444
> > 0.460317 0.476190 0.492063 0.507937 0.523810 0.539683 0.555556 0.571429
> > 0.58331 0.603175 0.619048 0.634921 0.650794 0.666667 0.682540 0.698413
> > 0.714286 0.730159 0.746032 0.761905 0.777778 0.793651 0.809524 0.825397
> > 0.841270 0.857143 0.873016 0.888889 0.904762 0.920635 0.936508 0.952381
> > 0.968254 0.984127 1.000000
> > mass-lambdas = 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000
> > coul-lambdas = 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000
> > restraint-lambdas = 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> > 0.000000 0.000000 0.000000 0.000000
> >
> > ; This makes sure we print out the differences in Hamiltonians between
> all
> > states, and not just the neighboring states
> > ;--------
> > calc-lambda-neighbors = -1
> >
> > ; the frequency the free energy information is calculated. This
> > ; frequency (every 0.2 ps) is pretty good for small molecule solvation.
> > ;-------
> > nstdhdl = 1000
> > ; not required, but useful if you are doing any temperature reweighting.
> > Without
> > ; temperature reweighting, you don't need the total energy -- differences
> > are enough
> > dhdl-print-energy = yes
> >
> > ; We are doing free energies with the LIPO_MUT molecule alone
> > couple-moltype = LIPO_MUT
> > ; we are mutating on type of molecule into another. In the initial
> state,
> > both are on
> > couple-lambda0 = vdw-q
> > ; in the final state, both are on.
> > couple-lambda1 = vdw-q
> > ; let the intramolecular interaction be coupled too
> > couple-intramol = yes
> >
> > ; expanded ensemble stuff
> > nstexpanded = 100
> > ; Wang-Landau algorithm to determine the free energies 'weights' of the
> > states
> > lmc-stats = wang-landau
> > ; Metropolized gibbs algorithm to move between states
> > lmc-move = metropolized-gibbs
> > ; we stop equilibrating when the wang-landau scaling term gets as low as
> > 0.0001
> > lmc-seed = 7890
> > lmc-weights-equil = wl-delta
> > weight-equil-wl-delta = 0.0001
> >
> > ; Seed for Monte Carlo in lambda space
> > ; We scale our wang landau weight by 0.7, whenever the smallest state
> > ; and largest state have ratio of 0.8. The initial wang-landau weight
> > ; increment delta is 1 kbT, and when this delta<1/N, where N is the
> > ; number of attempted switches in state space, we use 1/N as the delta,
> > ; which is less prone to saturation (stopping at the wrong value because
> > ; the weight schedule lowered too quickly).
> > wl-scale = 0.7
> > wl-ratio = 0.8
> > init-wl-delta = 1 ; this is 1*kB*T
> > wl-oneovert = yes
> >
> > ; frequency to output transition matrix
> > nst-transition-matrix = 10000000
> >
> > Any idea?
> >
> > Thanks,
> > Dejun
> > --
> > 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/Support/Mailing_Lists/Search before posting!
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>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 31 Jul 2013 14:20:47 -0700 (PDT)
> From: Sanku M <msanku65 at yahoo.com>
> Subject: [gmx-users] fatal error with charmm/amber forcefield
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <1375305647.17908.YahooMailNeo at web162013.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Dear Gromacs users,
> I am using gromacs 4.5.4 .
> Is there any known issue/problem in running hamiltonian replica exchange
> calculations or FEP with charm27.ff or amber forcefield in gromacs4.5.4 ?
> I tried running an hamiltonian replica exchange using charmm27.ff by
> interpolating A state and B state but it gives error that dihedral terms
> with multiple values can not be interpolated..One need to write all A and B
> states in topol.top manually.
> With opls.ff , it does not have any such problem. It works fine... Is it
> resolved in gromacs 4.6
>
> This is the series error I am getting when using charmm forcefield or
> amber forcefield:
> WARNING 1197 [file topol_scale.top, line 2353]:
> No default Proper Dih. types for perturbed atoms, using normal values
>
>
> ERROR 323 [file topol_scale.top, line 2354]:
> Cannot automatically perturb a torsion with multiple terms to different
> form.
> Please specify perturbed parameters manually for this torsion in your
> topology!
> Any idea?
> Thanks
> Sanku
>
> ------------------------------
>
> Message: 5
> Date: Wed, 31 Jul 2013 21:15:30 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: inconsistent energy drops
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51F9B6B2.8040507 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 7/31/13 4:45 PM, Brad Van Oosten wrote:
> > looking at the first 2 peaks, they are created from single outlying
> points in
> > the trajectory. Visually, I can see no discernible difference between it
> and
> > the frame before/after with the higher energy.
> >
>
> To find the source, you'll probably have to further decompose the energy
> terms
> using energygrps. Hard to say whether anything is wrong without first
> figuring
> out the (potentially) problematic term. It remains entirely possible that
> what
> you're seeing is entirely normal, you just have to line up behavior with
> observation.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==================================================
>
>
> ------------------------------
>
> --
> 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/Support/Mailing_Lists/Search before posting!
>
> End of gmx-users Digest, Vol 112, Issue 1
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