Thanks for the answer. PME can't be used since the interaction coulomb LR value between two groups can't be extracted for PME. I know switched cutoffs produce artefacts around the cutoff value but in this case I am more interested in the correct interaction energies than the correct forces which is why a shifted function can't be used. My plan was that with the rather large rcoulomb and rlist values I chose, a switched function would be ok.
Would the reaction field method suit my purposes? How do I choose epsilon_rf? I have pure water and 10M urea as solvents. Still I would like to figure out why switch creates these enormous fluctuations in my system. Can you see any errors in the parameters I've listed? Matteus -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: den 7 augusti 2009 14:51 To: [email protected] Subject: gmx-users Digest, Vol 64, Issue 39 Send gmx-users mailing list submissions to [email protected] 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 [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 gmx-users digest..." Today's Topics: 1. RE: System instability with switched cut-off (Berk Hess) 2. Re: Energy Minimisation and Equilibration Problems (Bruce D. Ray) 3. Re: question about mdrun -append (Baofu Qiao) ---------------------------------------------------------------------- Message: 1 Date: Fri, 7 Aug 2009 13:46:31 +0200 From: Berk Hess <[email protected]> Subject: RE: [gmx-users] System instability with switched cut-off To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Hi, Never ever use switched cut-off's! Switched cut-off's can give extremely strong artifacts. In 4.1 grompp will warn you about this. Switch gives you correct energies at short range, but incorrect forces in the switching region. What you want is correct forces up to (nearly) the cut-off. Shift does this. But reaction-field does this smoother and it even has a physical interpretation. So use RF if you can not use PME. But why can't you use PME, you have pbc, right? Berk From: [email protected] To: [email protected] Date: Fri, 7 Aug 2009 13:13:24 +0200 Subject: [gmx-users] System instability with switched cut-off Dear all Im trying to extract the interaction energies between protein and solvent. Since PME cant be used for this, plain cutoffs causes problems and shifted cut-offs gives incorrect energies I want to use switched cutoff but with rather long cutoffs to get the correct energy. Unfortunately my system is unstable and within a few ps the total energy and kinetic energy fluctuates several hundred per cent. I4ve tried different options but can4t get it to stabilize except if I4m using any other coulomb type. Any ideas? title = Dyna cpp = /usr/bin/cpp constraints = hbonds integrator = md dt = 0.002 nsteps = 20000000 nstxout = 20000000 nstvout = 20000000 nstfout = 5000 nstlog = 250 nstenergy = 500 nstxtcout = 500 xtc_grps = energygrps = polar hydrophobic peptide SOL nstlist = 1 ns_type = grid coulombtype = switch rcoulomb_switch = 1.4 rcoulomb = 1.7 rlist = 2.0 vdwtype = switch rvdw_switch = 1.4 rvdw = 1.7 tcoupl = nose-hoover tc-grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 298 298 Pcoupl = parrinello-rahman tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ;disre_fc = 30 gen_vel = yes gen_temp = 298 gen_seed = 173529 unconstrained_start = no Thanks Matteus --------------------------------------------------------- Matteus Lindgren, graduate student Department of Chemistry, Umee University SE-901 87 Umee, Sweden Phone: +46 (0)90-7865368 _________________________________________________________________ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090807/6c0d63c8/a ttachment-0001.html ------------------------------ Message: 2 Date: Fri, 7 Aug 2009 05:06:02 -0700 (PDT) From: "Bruce D. Ray" <[email protected]> Subject: Re: [gmx-users] Energy Minimisation and Equilibration Problems To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" On Thursday, August 6, 2009 at 7:59:43 PM Nancy <[email protected]> wrote: > I ran the minimisation, and mdrun gave the following last few lines of output: > > ================================== > Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395 > Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395 > Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom= 2395 > Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom= 2395 > Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom= 2395 > Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom= 2395 > Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom= 2395 > Step=19999, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom= 2395 > Step=20000, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom= 2395 > > writing lowest energy coordinates. > > Steepest Descents did not converge to Fmax < 10 in 20001 steps. > Potential Energy = -7.1493609e+04 > Maximum force = 2.4185994e+04 on atom 2395 > Norm of force = 8.1511212e+02 > ================================== > > As you can be seen, the forces still do not converge to Fmax < 10, even after 20,000 steps. > > Does anyone know what the problem might be? The problem is my error in the specification of non-bonded interaction combination rules, FudgeLJ, and FudgeQQ for gromacs force fields. Line 7 of your file ffethanediol.itp currently reads: 1 2 yes 0.5 0.833333 This was taken from ambconv and is correct for amber and gaff force fields, but not for gromacs force fields, nor for OPLS-AA. Change line 7 of the file ffethanediol.itp to read: 1 1 no 1.0 1.0 The correction is in topolbuild 1.3 which is not yet released, but this error was not caught for the topolbuild 1.2 series. Quite frankly, I had forgotten that modification was made as I've been editing the set of tables needed to add OPLS-AA to the mix of force fields available. As a general note. For gromacs force field topologies generated with anything in the topolbuild 1.2 series, this edit to the itp file that specifies the defaults is required. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090807/e002422d/a ttachment-0001.html ------------------------------ Message: 3 Date: Fri, 07 Aug 2009 14:49:45 +0200 From: Baofu Qiao <[email protected]> Subject: Re: [gmx-users] question about mdrun -append To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090807/ee691be4/a ttachment.html ------------------------------ _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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