--- On Tue, 9/2/16, Mehreen Jan <[email protected]> wrote:
> From: Mehreen Jan <[email protected]> > Subject: wrong number of control atomes in hdb > To: "Mehreen Jan" <[email protected]> > Received: Tuesday, 9 February, 2016, 2:44 PM > > -------------------------------------------- > On Tue, 9/2/16, Mehreen Jan <[email protected]> > wrote: > > Subject: Re: gromacs.org_gmx-users Digest, Vol 142, Issue > 42 > To: [email protected] > Received: Tuesday, 9 February, 2016, 2:43 PM > > Subject: Fw: wrong number of control > atomes in > > hdb > > > > > > > > > > respected sir! > > > > > thank you for advise > > > > > > > > > > thank you sir for advise i just copy > folder > > 43A1p > > > and > > > > past > > > > > in top file and in GMXLIB and it work > error > > is > > > solved > > > > know > > > > > after running the command: > > > > > pdb2gmx -f protein.top -o > protein.gro > > > > > select the forcefield 43A1p the > following > > error > > > is > > > > occurs > > > > > i google it but i can't get it exactly > and i > > read > > > > manual but > > > > > difficult to understand because of > no > > experience > > > . > > > > > respected sir kiendle find the > attachment . > > > > > > > > > > > > > > > error in hdb file > > ./gromacs43A1p/aminoacid.hdb: > > > > > > > > > > wrong number of control atoms (2 iso3) > on > > line: > > > > > 2 3 N -C -CA > -------------------------------------------- > On Tue, 9/2/16, [email protected] > <[email protected]> > wrote: > > Subject: gromacs.org_gmx-users Digest, Vol 142, Issue > 42 > To: [email protected] > Received: Tuesday, 9 February, 2016, 1:20 PM > > Send gromacs.org_gmx-users mailing > list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, > visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body > 'help' > to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is > more > specific > than "Re: Contents of gromacs.org_gmx-users > digest..." > > > Today's Topics: > > 1. Different results for same protein's > simulation in 4.6.5 and > 5.0.4 (SAPNA BORAH) > 2. Re: Different results for same > protein's simulation in 4.6.5 > and 5.0.4 (Mark Abraham) > 3. Re: creating representative structures > (Mark Abraham) > 4. Re: pp/pme ratio differences between > gromacs 5.0.x and 5.1.x > (Mark Abraham) > 5. Re: Fwd: FW: PME settings in free > energy calculations > (Mark Abraham) > > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 9 Feb 2016 12:52:41 +0530 > From: SAPNA BORAH <[email protected]> > To: [email protected] > Subject: [gmx-users] Different results for same > protein's > simulation > in 4.6.5 and 5.0.4 > Message-ID: > <cael2jf7tnt94mnmbw3h6ynskl63tc0+xezqhmfnre7wvpng...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear all, > > I have tried running the same protein in the two > versions > of > gromacs 4.6.5 > and 5.0.4. Now, both the runs are producing entirely > different results. > > The results till equilibration are same. > > After the run however, there is a total change in > the > production results. I > have used the same mdp files. > > I have rerun the systems and they still produce > similar > results in the same > version. > > The protein structure is a modelled one. > > > Thanks in advance. > Sapna. > > Sapna Mayuri Borah > c/o Dr. A. N. Jha > Research student > Tezpur University, > India > > > ------------------------------ > > Message: 2 > Date: Tue, 09 Feb 2016 07:37:54 +0000 > From: Mark Abraham <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] Different results for same > protein's > simulation in 4.6.5 and 5.0.4 > Message-ID: > > <CAMNuMARf1tJD+thVQvoSuN9SPkYhW06Oo2w6=bbfh6udvfs...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi, > > This is quite normal. > > http://www.gromacs.org/Documentation/Terminology/Reproducibility. > You > should see a similar range of variation in the > trajectories > produced in the > two versions that are incompletely sampling the same > ensemble, but one can > say very little about two single observed > trajectories > sampled from them. > > Mark > > On Tue, Feb 9, 2016 at 8:23 AM SAPNA BORAH <[email protected]> > wrote: > > > Dear all, > > > > I have tried running the same protein in the > two > versions of gromacs 4.6.5 > > and 5.0.4. Now, both the runs are producing > entirely > different results. > > > > The results till equilibration are same. > > > > After the run however, there is a total change > in the > production results. I > > have used the same mdp files. > > > > I have rerun the systems and they still produce > similar > results in the same > > version. > > > > The protein structure is a modelled one. > > > > > > Thanks in advance. > > Sapna. > > > > Sapna Mayuri Borah > > c/o Dr. A. N. Jha > > Research student > > Tezpur University, > > India > > -- > > 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 [email protected]. > > > > > ------------------------------ > > Message: 3 > Date: Tue, 09 Feb 2016 07:46:31 +0000 > From: Mark Abraham <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] creating representative > structures > Message-ID: > <camnumaqgbnhazsinyedzpldwezdunsbdmz77bljho5qkt7w...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi, > > On Mon, Feb 8, 2016 at 6:24 PM Shyno Mathew <[email protected]> > wrote: > > > Dear all, > > > > > > I have few questions regarding creating > representative > structures. For > > simplicity, let?s say I have a trajectory of 5 > frames: > > > > 1. g_rmsf: After reading > previous posts, here is what I understood. > > The average structures calculated using g_rmsf > (by > specifying ?ox) is > > literally the average of x, y, z co-ordinates of > each > atom over all the 5 > > frames in my case. Energy minimizing this > averaged > structure might give a > > meaningful structure? > > > > It'll give a structure that conforms to chemical > expectations, but the > "meaning" of any plausible candidate for an > "average" > structure is doubtful > at best. If there is a group of microstates that > share > structural > similarity, it does not follow that RMSD will > identify it, > nor that > averaging of coordinates will produce a meaningful > average. > What is the RMS > average position of a set of balls being juggled? > > > > 2. g_cluster: Here I am > using the gromos method. I read the reference > > paper (Daura et al.). Using gromos method and by > just > specifying ?cl (not > > ?av) I get the middle structures for each > cluster. > Let?s say I get 2 > > clusters using rmsd 0.16. Now the > representative > structures of these two > > clusters (obtained in the out.pdb) should > exactly > correspond to two frames > > in my original trajectory (the one with 5 > frames)? > > > > I don't know, but you should try it and see. Make a > trajectory of a water > molecule as PDB with a few frames and play with > editing > the > coordinates by > hand and passing them to g_cluster until you are > happy you > understand how > it works. > > > > 3. My final question is > regarding how exactly g_cluster works, here > > is what I understand from Daura et al. > > > > If I use g_cluster with gromos method, the code > will > look for neighbors of > > each frame within specified cutoff. > > > > Assume the first time the code finds the > following: > > > > frame 0 has two neighbors: frames 2,3 within > cutoff > > > > frame 1 has three neighbors: frames 2, 3, 4 > within > cutoff > > > > frame 2 has four neighbors: frames 0, 1, 3, 4 > within > cutoff > > > > frame 3 has three neighbors: frames 0,1, 2 > within > cutoff > > > > frame 4 has two neighbors: frames 1,2 within > cutoff > > > > > > > > Since frame 2 has the highest number of > neighbors, > it's > considered the > > center cluster and this frame along with > neighbors > are > removed. The same > > calculation is performed on the remaining frames > if I > had more frames. > > > > No idea, but again try it and see. > > Mark > > > > Thanks in advance for your help, > > > > Sincerely, > > > > Shyno > > > > -- > > Shyno Mathew > > PhD Candidate > > Department of Chemical Engineering > > Graduate Assistant > > Office of Graduate Student Affairs > > The Fu Foundation School Of Engineering and > Applied > Science > > Columbia University > > -- > > 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 [email protected]. > > > ------------------------------ > > Message: 4 > Date: Tue, 09 Feb 2016 07:59:18 +0000 > From: Mark Abraham <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] pp/pme ratio differences > between > gromacs > 5.0.x and 5.1.x > Message-ID: > <camnumarebaeycg6fok-3mg5w0p4nuwats93xqvy6ge3ngpp...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi, > > On Sun, Feb 7, 2016 at 8:00 PM Johannes Wagner <[email protected]> > wrote: > > > hey guys, > > came across an issue with pp/pme ratio > difference > from > 5.0 to 5.1. For a > > system running on 2 nodes with a pp/pme ratio > of > 80:16 > on 5.0, the same > > thing starts with 72:24 on gromacs 5.1. The 5.1 > run > has > a much higher load > > imbalance and is hence slower. Are there known > changes > from 5.0 to 5.1 in > > the pp/pme ratio that cause this? > > > > Yes and no. Even on only two nodes, your observations > can > be > affected by > network congestion, so I would investigate whether > you can > reproduce the > observations. The changes that I identified that had > the > capacity to change > performance are noted at > > http://manual.gromacs.org/documentation/5.1/ReleaseNotes/performance.html. > For example, if you're using LINCS then the SIMD > improvements there affect > only the PP ranks so it might seem to the auto-tuner > that > it's more > efficient to use fewer PP ranks. Then later some kind > of > load imbalance has > a stronger effect. The interactions of DD DLB and > PME > tuning > are complex, > and we can't rule out that there's a problem that we > should > fix. But we > can't say much without being able to compare some > (reproducible) log files. > > Mark > > cheers, johannes > > > > -- > > 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 [email protected]. > > > > > ------------------------------ > > Message: 5 > Date: Tue, 09 Feb 2016 08:20:17 +0000 > From: Mark Abraham <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] Fwd: FW: PME settings in > free > energy > calculations > Message-ID: > <CAMNuMAQ9oJbDrAuW9danqaXXmhTNw=zsjxz9s-tdw9warsr...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi, > > On Fri, Feb 5, 2016 at 1:32 PM Dries Van Rompaey > <[email protected]> > wrote: > > > Hi, > > > > The corresponding mdp output section is: > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing electrostatics > > coulombtype > = PME > > coulomb-modifier > = Potential-shift-Verlet > > rcoulomb-switch = 0 > > rcoulomb > = 1.0 > > ; Relative dielectric constant for the medium > and the > reaction field > > epsilon-r > = 1 > > epsilon-rf > = 0 > > ; Method for doing Van der Waals > > vdwtype > = cutoff > > vdw-modifier > = Potential-switch > > ; cut-off lengths > > rvdw-switch > = 0.9 > > rvdw > = 1.0 > > ; Apply long range dispersion corrections for > Energy > and Pressure > > DispCorr > = EnerPres > > ; Extension of the potential lookup tables > beyond the > cut-off > > table-extension = 1 > > ; Separate tables between energy group pairs > > energygrp-table = > > ; Spacing for the PME/PPPM FFT grid > > fourierspacing > = 0.08 > > ; FFT grid size, when a value is 0 > fourierspacing > will > be used > > fourier-nx > = 0 > > fourier-ny > = 0 > > fourier-nz > = 0 > > ; EWALD/PME/PPPM parameters > > pme_order > = 6 > > ewald_rtol > = 1e-06 > > ewald-rtol-lj > = 0.001 > > lj-pme-comb-rule > = Geometric > > ewald-geometry > = 3d > > epsilon_surface = 0 > > > That all seems reasonable. > > > > I evaluated the energy with: > > > > Verlet - settings above (with standard > verlet-buffer-tolerance) > > @ s0 legend "Coulomb-14" > > @ s1 legend "Coulomb (SR)" > > @ s2 legend "Coul. recip." > > 0.000000 > -2221.295898 -546205.250000 9271.518555 > > Total - 539155.0273 > > > > Verlet - settings above - with > verlet-buffer-tolerance > -1 > > 0.000000 > -2221.295898 -546205.250000 9271.516602 > > Total -539155.029296 > > > > That kind of agreement is expected, but perhaps > might > agree > exactly if you > were following > http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy > > Group - settings above > > @ s0 legend "Coulomb-14" > > @ s1 legend "Coulomb (SR)" > > @ s2 legend "Coul. recip." > > 0.000000 > -2221.296387 -487993.593750 -48931.437500 > > Total -539146.3276 > > > > The difference in those components is expected - in > PME > you > have to avoid > counting contributions in the long-range part from > pairs > that are excluded > e.g. from the bonded topology. The two schemes handle > this > in different > places. Their sum should match (within the limits of > floating-point > arithmetic), and a relative error under 1e-5 for > summing a > few million > numbers is acceptable for judging the equivalence of > the > implementations. > > Verlet - 3 nm cutoffs, 2.9 vdwswitch, > coulomb-modifier > none > > @ s0 legend "Coulomb-14" > > @ s1 legend "Coulomb (SR)" > > 0.000000 > -2221.295898 -774817.875000 > > Total -777039.1709 > > > > > > Group - 3 nm cutoffs, 2.9 vdwswitch, > coulomb-modifier > none > > @ s0 legend "Coulomb-14" > > @ s1 legend "Coulomb (SR)" > > 0.000000 > -2221.296387 -553398.125000 > > Total -555619.4214 > > > > That ought to agree much better, but It's hard to > speculate > on where the > problem lies without seeing log files. Please upload > some > to > a file sharing > service and post the links here (list doesn't take > attachments) > > Mark > > > > Thanks, > > > > Dries > > > > On 4 February 2016 at 14:48, Michael Shirts > <[email protected]> > wrote: > > > > > Also, can you be more precise about the > inconsistency in the outputs > > > you are seeing (with numerical output from > GROMACS > and analysis code). > > > > > > On Thu, Feb 4, 2016 at 6:17 AM, Michael > Shirts > <[email protected]> > > wrote: > > > > Hi, Dries- > > > > > > > > Can you print out what the > corresponding > section of mdout.mdp look > > like? > > > > > > > > Have you tried using the cutoffs > above > with group cutoffs, and seen > > > > what the difference is? > > > > > > > > On Thu, Feb 4, 2016 at 4:59 AM, Dries > Van > Rompaey > > > > <[email protected]> > wrote: > > > >> Hi, > > > >> > > > >> I'm using PME with the default > Potential-Shift-Verlet modifier. If I'm > > > >> interpreting the manual and > comments on > the mailinglist correctly, the > > > >> settings for rcoulomb-switch > shouldn't > affect this and PME-switching > > > >> shouldn't be necessary (although > there > seems to have been some > > > discussion > > > >> about this, https://gerrit.gromacs.org/#/c/2220/). Has a consensus > > been > > > >> reached elsewhere? > > > >> > > > >> Current nonbonded settings in my > .mdp > files are: > > > >> ; Electrostatics > > > >> coulombtype > = PME > > > >> rcoulomb > = 1.0 > > > >> > > > >> ; van der Waals > > > >> vdwtype > = cutoff > > > >> vdw-modifier > = Potential-switch > > > >> rvdw-switch > = 0.9 > > > >> rvdw > > = 1.0 > > > >> > > > >> ; Apply long range dispersion > corrections > for Energy and Pressure > > > >> DispCorr > = EnerPres > > > >> > > > >> ; Spacing for the PME/PPPM FFT > grid > > > >> fourierspacing > = 0.08 > > > >> > > > >> ; EWALD/PME/PPPM parameters > > > >> pme_order > = 6 > > > >> ewald_rtol > = 1e-06 > > > >> epsilon_surface > = 0 > > > >> > > > >> Thanks in advance, > > > >> > > > >> Dries > > > >> > > > >> On 4 February 2016 at 00:56, > Michael > Shirts <[email protected]> > > wrote: > > > >> > > > >>> Hi, Dries- > > > >>> > > > >>> Questions like this are > probably > best > answered on the gmx-users list. > > > >>> I can't say too much for the > Verlet > scheme -- I know that it was > > > >>> relatively recently adapted > for > free > energies, and there may be some > > > >>> combinations of settings that > could > give unanticipated results. > > > >>> > > > >>> Pretty much all of our > experience > about nonbonded calculations and > > > >>> free energies is collected in > the > following paper: > > > >>> http://pubs.acs.org/doi/abs/10.1021/ct4005068. We used > the group > > > >>> cutoff scheme since that was > the > only > one that was supported in > > > >>> GROMACS at the time. > > > >>> > > > >>> Since you haven't sent any > files, > it's hard to tell what is actually > > > >>> going on. The one thing that > has a > tendency to happen with the more > > > >>> recent update schemes is if > you set > a > potential modifier that is a > > > >>> switch, but don't set the > distance > the switch starts at, then it is > > > >>> automatically set to zero. > Check the mdout.mdp to see if this is > > > >>> happening. > > > >>> > > > >>> > From: Van Rompaey Dries > <[email protected]> > > > >>> Date: Wednesday, February 3, > 2016 > at > 12:34 PM > > > >>> To: Michael Shirts <[email protected]> > > > >>> Subject: PME settings in free > energy > calculations > > > >>> > > > >>> Dear prof. Shirts, > > > >>> > > > >>> I'm currently trying to figure > out > the PME settings for a relative > > > >>> free binding energy simulation > I'm > working on. I took the parameters > > > >>> from Matteo Aldeghi's > > > >>> paper( > > > >>> > > > > > > http://pubs.rsc.org/en/content/articlelanding/2015/sc/c5sc02678d#!divAbstract > > > >>> ) > > > >>> as a starting point (adapted > for > the > Verlet scheme by scaling the > > > >>> fourierspacing to 0.08 and > setting > coulomb = rvdw = 1.0). I then > > tried > > > >>> to verify these settings by > comparing > a single point energy > > > >>> calculation with these > settings and > one with very long coulomb > > cutoffs > > > >>> as recommended on > alchemistry.org. > > > >>> > > > >>> Unfortunately, I can't seem to > get > this quite right. I'm getting > > > >>> differences in the hundreds > of > kj/mol, leading me to suspect I'm > > doing > > > >>> something wrong. I'm > calculating > the > energy values by extracting > > > >>> CoulombSR and Coul-recip from > the > energy.xvg files. I've tried > > > >>> calculating the energy with > coulomb > cutoffs at 3 nm and 10 nm, but > > > >>> agreement with the PME > results > remains rather poor. David Mobley > > > >>> mentioned you performed > extensive > research on this topic, and I'm > > > >>> hoping you could point me in > the > right direction. > > > >>> > > > >>> Thanks in advance, > > > >>> > > > >>> Dries > > > >>> > > > >>> > > > >>> > > > >>> ~~~~~~~~~~~~~~~~ > > > >>> Michael Shirts > > > >>> Associate Professor > > > >>> [email protected] > > > >>> Phone: (303) 735-7860 > > > >>> Office: JSCBB D317 > > > >>> Department of Chemical and > Biological > Engineering > > > >>> University of Colorado > Boulder > > > >>> -- > > > >>> 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 [email protected]. > > > >>> > > > >> -- > > > >> 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 [email protected]. > > > -- > > > 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 [email protected]. > > > > > -- > > 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 [email protected]. > > > > > ------------------------------ > > -- > 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 [email protected]. > > End of gromacs.org_gmx-users Digest, Vol 142, Issue > 42 > > ****************************************************** -- 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 [email protected].
