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-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 <jalem...@vt.edu> > Subject: Re: [gmx-users] Interaction energy between specific residue > in a set of residues > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <51f97348.1010...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > > > ------------------------------ > > Message: 2 > Date: Wed, 31 Jul 2013 13:45:02 -0700 (PDT) > From: Brad Van Oosten <bv0...@brocku.ca> > Subject: [gmx-users] Re: inconsistent energy drops > To: gmx-users@gromacs.org > Message-ID: <1375303502523-5010267.p...@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 <mrshi...@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@gromacs.org> > Message-ID: > <CA+zJb=gQY5BdJ_L9P_+nAnQhiWGe0nR+xEqZ7Pvf-UWiEq-H= > g...@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....@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@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! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ------------------------------ > > Message: 4 > Date: Wed, 31 Jul 2013 14:20:47 -0700 (PDT) > From: Sanku M <msank...@yahoo.com> > Subject: [gmx-users] fatal error with charmm/amber forcefield > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: > <1375305647.17908.yahoomail...@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 <jalem...@vt.edu> > Subject: Re: [gmx-users] Re: inconsistent energy drops > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <51f9b6b2.8040...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@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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