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Please believe me, switched Coulomb potential are very bad!<br><br>I understand you want to have the energies correct,<br>but the first thing you want is the forces to be correct.<br>The forces matter for your sampling.<br>If you use a switch function you will always have artificially<br>large forces in the switching region. Switching between 1.4 and 1.7 nm<br>switches over 0.3 nm. This produces much larger forces than the plain<br>Coulomb ones around say 0.5 nm.<br><br>For RF I would always use epsilon_rf=infinity (0 in the mdp file).<br>This makes sure the potential and force are zero at the cut-off.<br>Because RF also applies to exclusions, energies are the same as with PME<br>up to many digits in systems without ionic groups.<br><br>Another option would be running with PME and using mdrun -rerun with<br>a long Coulomb cut-off.<br><br>Berk<br><br>> From: matteus.lindgren@chem.umu.se<br>> To: gmx-users@gromacs.org<br>> Date: Fri, 7 Aug 2009 15:51:47 +0200<br>> Subject: [gmx-users] RE: System instability with switched cut-off<br>> <br>> Thanks for the answer. PME can't be used since the interaction coulomb LR<br>> value between two groups can't be extracted for PME. I know switched cutoffs<br>> produce artefacts around the cutoff value but in this case I am more<br>> interested in the correct interaction energies than the correct forces which<br>> is why a shifted function can't be used. My plan was that with the rather<br>> large rcoulomb and rlist values I chose, a switched function would be ok. <br>> <br>> Would the reaction field method suit my purposes? How do I choose<br>> epsilon_rf? I have pure water and 10M urea as solvents. Still I would like<br>> to figure out why switch creates these enormous fluctuations in my system.<br>> Can you see any errors in the parameters I've listed?<br>> <br>> Matteus<br>> <br>> <br>> -----Original Message-----<br>> From: gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]<br>> On Behalf Of gmx-users-request@gromacs.org<br>> Sent: den 7 augusti 2009 14:51<br>> To: gmx-users@gromacs.org<br>> Subject: gmx-users Digest, Vol 64, Issue 39<br>> <br>> Send gmx-users mailing list submissions to<br>> gmx-users@gromacs.org<br>> <br>> To subscribe or unsubscribe via the World Wide Web, visit<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> or, via email, send a message with subject or body 'help' to<br>> gmx-users-request@gromacs.org<br>> <br>> You can reach the person managing the list at<br>> gmx-users-owner@gromacs.org<br>> <br>> When replying, please edit your Subject line so it is more specific<br>> than "Re: Contents of gmx-users digest..."<br>> <br>> <br>> Today's Topics:<br>> <br>> 1. RE: System instability with switched cut-off (Berk Hess)<br>> 2. Re: Energy Minimisation and Equilibration Problems (Bruce D. Ray)<br>> 3. Re: question about mdrun -append (Baofu Qiao)<br>> <br>> <br>> ----------------------------------------------------------------------<br>> <br>> Message: 1<br>> Date: Fri, 7 Aug 2009 13:46:31 +0200<br>> From: Berk Hess <gmx3@hotmail.com><br>> Subject: RE: [gmx-users] System instability with switched cut-off<br>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> Message-ID: <COL113-W42EEC13FE2DE71D0118E668E0B0@phx.gbl><br>> Content-Type: text/plain; charset="iso-8859-1"<br>> <br>> <br>> Hi,<br>> <br>> Never ever use switched cut-off's!<br>> Switched cut-off's can give extremely strong artifacts.<br>> In 4.1 grompp will warn you about this.<br>> <br>> Switch gives you correct energies at short range, but incorrect forces<br>> in the switching region.<br>> What you want is correct forces up to (nearly) the cut-off.<br>> Shift does this.<br>> But reaction-field does this smoother and it even has a physical<br>> interpretation.<br>> So use RF if you can not use PME.<br>> <br>> But why can't you use PME, you have pbc, right?<br>> <br>> Berk<br>> <br>> <br>> From: matteus.lindgren@chem.umu.se<br>> To: gmx-users@gromacs.org<br>> Date: Fri, 7 Aug 2009 13:13:24 +0200<br>> Subject: [gmx-users] System instability with switched cut-off<br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> Dear all<br>> <br>> <br>> <br>> Im trying to extract the interaction<br>> energies between protein and solvent. Since PME cant be used for this, plain<br>> cutoffs causes problems and shifted cut-offs gives incorrect energies I want<br>> to<br>> use switched cutoff but with rather long cutoffs to get the correct energy. <br>> <br>> <br>> <br>> Unfortunately my system is unstable and<br>> within a few ps the total energy and kinetic energy fluctuates several<br>> hundred<br>> per cent. I4ve tried different options but can4t get it to stabilize except<br>> if<br>> I4m using any other coulomb type. Any ideas?<br>> <br>> <br>> <br>> title =<br>> Dyna<br>> <br>> cpp =<br>> /usr/bin/cpp<br>> <br>> constraints =<br>> hbonds<br>> <br>> integrator =<br>> md<br>> <br>> dt =<br>> 0.002<br>> <br>> nsteps =<br>> 20000000<br>> <br>> nstxout =<br>> 20000000<br>> <br>> nstvout =<br>> 20000000<br>> <br>> nstfout =<br>> 5000<br>> <br>> nstlog =<br>> 250<br>> <br>> nstenergy =<br>> 500<br>> <br>> nstxtcout =<br>> 500<br>> <br>> xtc_grps = <br>> <br>> energygrps =<br>> polar hydrophobic peptide SOL <br>> <br>> nstlist = 1<br>> <br>> ns_type =<br>> grid<br>> <br>> coulombtype =<br>> switch<br>> <br>> rcoulomb_switch =<br>> 1.4<br>> <br>> rcoulomb =<br>> 1.7<br>> <br>> rlist =<br>> 2.0<br>> <br>> vdwtype =<br>> switch<br>> <br>> rvdw_switch =<br>> 1.4<br>> <br>> rvdw =<br>> 1.7<br>> <br>> tcoupl =<br>> nose-hoover<br>> <br>> tc-grps = Protein <br>> Non-Protein<br>> <br>> tau_t =<br>> 0.5 0.5<br>> <br>> ref_t =<br>> 298 298<br>> <br>> Pcoupl =<br>> parrinello-rahman<br>> <br>> tau_p =<br>> 1.0<br>> <br>> compressibility =<br>> 4.5e-5<br>> <br>> ref_p =<br>> 1.0<br>> <br>> <br>> <br>> ;disre_fc =<br>> 30<br>> <br>> <br>> <br>> gen_vel = yes<br>> <br>> gen_temp = 298<br>> <br>> gen_seed = 173529<br>> <br>> unconstrained_start <br>> = no<br>> <br>> <br>> <br>> Thanks<br>> <br>> Matteus <br>> <br>> <br>> <br>> --------------------------------------------------------- <br>> <br>> Matteus<br>> Lindgren, graduate student<br>> <br>> Department of Chemistry, Umee University <br>> <br>> SE-901 87 Umee, Sweden<br>> <br>> Phone: +46 (0)90-7865368 <br>> <br>> <br>> <br>> <br>> <br>> <br>> _________________________________________________________________<br>> See all the ways you can stay connected to friends and family<br>> http://www.microsoft.com/windows/windowslive/default.aspx<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL:<br>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20090807/6c0d63c8/a<br>> ttachment-0001.html<br>> <br>> ------------------------------<br>> <br>> Message: 2<br>> Date: Fri, 7 Aug 2009 05:06:02 -0700 (PDT)<br>> From: "Bruce D. Ray" <brucedray@yahoo.com><br>> Subject: Re: [gmx-users] Energy Minimisation and Equilibration<br>> Problems<br>> To: gmx-users@gromacs.org<br>> Message-ID: <664136.39384.qm@web35807.mail.mud.yahoo.com><br>> Content-Type: text/plain; charset="us-ascii"<br>> <br>> On Thursday, August 6, 2009 at 7:59:43 PM Nancy <nancy5villa@gmail.com><br>> wrote:<br>> <br>> <br>> > I ran the minimisation, and mdrun gave the following last few lines of<br>> output:<br>> > <br>> > ==================================<br>> > Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom=<br>> 2395<br>> > Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom=<br>> 2395<br>> > <br>> Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom=<br>> 2395<br>> > Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom=<br>> 2395<br>> > Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom=<br>> 2395<br>> > <br>> Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom=<br>> 2395<br>> > Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom=<br>> 2395<br>> > Step=19999, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom=<br>> 2395<br>> > <br>> Step=20000, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom=<br>> 2395<br>> > <br>> > writing lowest energy coordinates.<br>> > <br>> > Steepest Descents did not converge to Fmax < 10 in 20001 steps.<br>> > Potential Energy = -7.1493609e+04<br>> > <br>> Maximum force = 2.4185994e+04 on atom 2395<br>> > Norm of force = 8.1511212e+02<br>> > ==================================<br>> > <br>> > As you can be seen, the forces still do not converge to Fmax < 10, even<br>> after 20,000 steps.<br>> > <br>> > Does anyone know what the problem might be?<br>> <br>> The problem is my error in the specification of non-bonded interaction<br>> combination rules,<br>> FudgeLJ, and FudgeQQ for gromacs force fields.<br>> <br>> Line 7 of your file ffethanediol.itp currently reads:<br>> 1 2 yes 0.5 0.833333<br>> <br>> This was taken from ambconv and is correct for amber and gaff force fields,<br>> but not<br>> for gromacs force fields, nor for OPLS-AA.<br>> <br>> Change line 7 of the file ffethanediol.itp to read:<br>> 1 1 no 1.0 1.0<br>> <br>> The correction is in topolbuild 1.3 which is not yet released, but this<br>> error was not caught<br>> for the topolbuild 1.2 series. Quite frankly, I had forgotten that<br>> modification was made as<br>> I've been editing the set of tables needed to add OPLS-AA to the mix of<br>> force fields available.<br>> <br>> As a general note. For gromacs force field topologies generated with<br>> anything in the<br>> topolbuild 1.2 series, this edit to the itp file that specifies the defaults<br>> is required.<br>> <br>> <br>> Sincerely,<br>> <br>> <br>> -- <br>> Bruce D. Ray, Ph.D.<br>> Associate Scientist<br>> IUPUI<br>> Physics Dept.<br>> 402 N. Blackford St.<br>> Indianapolis, IN 46202-3273<br>> <br>> <br>> <br>> <br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL:<br>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20090807/e002422d/a<br>> ttachment-0001.html<br>> <br>> ------------------------------<br>> <br>> Message: 3<br>> Date: Fri, 07 Aug 2009 14:49:45 +0200<br>> From: Baofu Qiao <qiaobf@gmail.com><br>> Subject: Re: [gmx-users] question about mdrun -append<br>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> Message-ID: <4A7C22E9.2080501@gmail.com><br>> Content-Type: text/plain; charset="us-ascii"<br>> <br>> An HTML attachment was scrubbed...<br>> URL:<br>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20090807/ee691be4/a<br>> ttachment.html<br>> <br>> ------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list<br>> gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> <br>> End of gmx-users Digest, Vol 64, Issue 39<br>> *****************************************<br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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