gromacs4.5.5 phosphorylated protein - protein-protein interaction phosphate at "SEP" and TPO forcefield 43A1p download from gromacs web page command: pdb2gmx -f protein.pdb -p protein.top -o protein.gro
fatal error: error in hdb file ./gromos43A1p.ff/aminoacid.hdb wrong number of control atoms (2 iso 3) on line: 2 3 N -C -CA i read manual but i can't remove error. i did not get the point how to remove error HDB file s given: ABU 1 1 1 H N -C CA ACEH 1 3 4 HA CA C O AIB 1 1 1 H N -C CA ALA 1 1 1 H N -C CA ARG 4 1 1 H N -C CA 1 1 HE NE CD CZ 2 3 HH1 NH1 CZ NE 2 3 HH2 NH2 CZ NE ARGN 4 1 1 H N -C CA 1 1 HE NE CD CZ 1 2 HH1 NH1 CZ NE 2 3 HH2 NH2 CZ NE ASN 2 1 1 H N -C CA 2 3 HD2 ND2 CG CB ASP 1 1 1 H N -C CA ASP1 2 1 1 H N -C CA 1 2 HD1 OD1 CG CB ASPH 2 1 1 H N -C CA 1 2 HD2 OD2 CG CB BEN 7 1 1 H2 C2 C1 C3 1 1 H3 C3 C2 C4 1 1 H4 C4 C3 C5 1 1 H5 C5 C4 C6 1 1 H6 C6 C5 C1 2 3 H1 N1 C7 C1 2 3 H2 N2 C7 C1 CYS2 1 1 1 H N -C CA CYSH 2 1 1 H N -C CA 1 2 HG SG CB CA FAD 7 2 3 HN6 AN6 AC6 AC5 1 2 HO2* AO2* AC2* AC1* 1 2 HO3* AO3* AC3* AC2* 1 2 H4* O4* C4* C5* 1 2 H3* O3* C3* C4* 1 2 H2* O2* C2* C3* 1 2 H3 N3 C4 C4A GLN 2 1 1 H N -C CA 2 3 HE2 NE2 CD CG GLU 1 1 1 H N -C CA GLUH 2 1 1 H N -C CA 1 2 HE2 OE2 CD CG GLY 1 1 1 H N -C CA HEME 4 1 1 HHA CHA C1A C4D 1 1 HHB CHB C1B C4A 1 1 HHC CHC C1C C4B 1 1 HHD CHD C1D C4C HIS1 2 1 1 H N -C CA 1 1 HD1 ND1 CG CE1 HISA 2 1 1 H N -C CA 1 1 HD1 ND1 CG CE1 HISB 2 1 1 H N -C CA 1 1 HE2 NE2 CE1 CD2 HISH 3 1 1 H N -C CA 1 1 HD1 ND1 CG CE1 1 1 HE2 NE2 CE1 CD2 HO4 1 3 10 HW OW HOH 1 2 7 HW OW HYP 1 1 2 HD1 OD1 CG CB ILE 1 1 1 H N -C CA LEU 1 1 1 H N -C CA LYS 2 1 1 H N -C CA 2 4 HZ NZ CE CD LYSH 2 1 1 H N -C CA 3 4 HZ NZ CE CD MET 1 1 1 H N -C CA NAC 1 1 1 H N -C CA NACH 2 1 1 H N -C CA 3 4 HA CA N NH NH2 1 2 3 H N -C -CA PHE 6 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 1 HZ CZ CE1 CE2 PHEU 1 1 1 H N -C CA PHL 7 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 1 HZ CZ CE1 CE2 1 2 HY OY CX CA SER 2 1 1 H N -C CA 1 2 HG OG CB CA TFE 1 1 2 H O CH2 C THR 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA TRP 7 1 1 H N -C CA 1 1 HD1 CD1 CG NE1 1 1 HE1 NE1 CD1 CE2 1 1 HE3 CE3 CD2 CZ3 1 1 HZ3 CZ3 CE3 CH2 1 1 HH2 CH2 CZ3 CZ2 1 1 HZ2 CZ2 CE2 CH2 TRPU 2 1 1 H N -C CA 1 1 HE1 NE1 CD1 CE2 TYR 6 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 2 HH OH CZ CE1 TYRU 2 1 1 H N -C CA 1 2 HH OH CZ CE1 VAL 1 1 1 H N -C CA SEP 1 1 1 H N -C CA TPO 1 1 1 H N -C CA PTR 5 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ SEPH 2 1 1 H N -C CA 1 2 H3P O3P P OG TPOH 2 1 1 H N -C CA 1 2 H3P O3P P OG1 PTRH 6 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 2 H3P O3P P OH thank you mehreen -------------------------------------------- On Tue, 9/2/16, [email protected] <[email protected]> wrote: Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 44 To: [email protected] Received: Tuesday, 9 February, 2016, 2:47 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. Fw: wrong number of control atomes in hdb (Mehreen Jan) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Feb 2016 09:47:18 +0000 (UTC) From: Mehreen Jan <[email protected]> To: <[email protected]> Subject: [gmx-users] Fw: wrong number of control atomes in hdb Message-ID: <[email protected]> Content-Type: text/plain; charset=UTF-8 --- 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? 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