Here is the mdp file title = HEX cpp = /lib/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 2500000 ; total 5ns. nstcomm = 10 nstxout = 50000 nstvout = 50000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off vdwtype = Cut-off rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = v-rescale tc_grps = HEX tau_t = 0.1 ref_t = 300 nsttcouple = 1 ; Energy monitoring energygrps = HEX ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps = BMI PFF tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5
; Generate velocites is off at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 100000 This is the 'averages' section " <=" ===== ######## ####### ==> " <=" === A V E R A G E S ====> " <=" = ############ ### ======> " St" atistics over 1 0000001 steps u sing 10000001 f rames Energies (kJ/mo l) Bond Angle Ry ckaert-Bell. LJ (SR) Coulomb (SR) 4.57E+03 3.62E+03 3.34E+03 -2.08E+04 0.00E+00 Potential Kinetic En. Total Energy Temperature Pressure (bar) -9.28E+03 1.63E+04 7.05E+03 3.00E+02 9.96E+02 Box-X Box-Y Box-Z 5.47E+00 5.47E+00 5.47E+00 Total Virial (k J/mol) 5.44E+02 -1.30E-01 8.27E-02 -1.30E-01 5.44E+02 3.46E-02 8.27E-02 3.46E-02 5.44E+02 Pressure (bar) 9.96E+02 2.34E-02 -1.51E-02 2.34E-02 9.96E+02 -2.77E-02 -1.51E-02 -2.77E-02 9.96E+02 Total Dipole (D ) 0.00E+00 0.00E+00 0.00E+00 I don't have an RMS section on my log file. The final xvg file that comes from g_energy is much too long to post here, but contains exactly what is in the log file. The interactive output from g_energy is, however, thus: Pressure = 995.9 bar (error = 0.65 bar) On Tue, Feb 1, 2011 at 1:49 PM, Justin A. Lemkul <[email protected]> wrote: > > > Denny Frost wrote: > >> Sorry to revisit this subject, but this output does not make sense. In >> the log file from my NPT simulation, the pressure readings fluctuate between >> about 300 bar and -300 bar, which I gather is pretty normal. However, at >> the end of the log file, it reports the average pressure being almost 1000 >> bar. g_energy also reports this value. In my mdp file, nstenergy is equal >> to nstlog, so the frequency of data is the same in the .edr file. How is is >> possible that the final average would be greater than any value obtained >> during the simulation? >> >> > As I recall from the previous discussion, there were lots of things wrong > with your .mdp file and many things to troubleshoot. Can you please post: > > 1. The .mdp file you're using > 2. The contents of the "AVERAGES" and "RMS FLUCTUATIONS" sections of your > .log file > 3. The g_energy output (not the header stuff, just the actual meaningful > result) > > -Justin > > On Thu, Jan 20, 2011 at 4:33 PM, Mark Abraham > <[email protected]<mailto: >> [email protected]>> wrote: >> >> On 21/01/2011 10:12 AM, Denny Frost wrote: >> >>> Sorry, I'm referring to a lot of runs here - some fluctuate more >>> than others and some have greater average values than others. The >>> average value is never greater than the maximum fluctuation in >>> each run, so that is not a problem. The average given by >>> g_energy, however, is not close to 1.0 bar in any of my runs. >>> Some runs give an average pressure of 10 bar, some give an >>> average value of -1000 bar. >>> >> >> In addition to all the points Justin mentioned, I'd observe that >> you're generating velocities at the start of the run, so the system >> will not be equilibrated for some time after that. See the advice >> here >> www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation >> < >> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation >> >. >> >> Anyway, you don't want to collect data for averages until after >> equilibration. >> >> Secondly, tau-t of 0.1 is useful for equilibration, but a bit too >> stringent for actual simulations. Using v-rescale T-coupling is >> probably a good idea too. >> >> Until you address all these issues about the numerical quality of >> your model of reality, hoping for observables to correlate with >> reality is not justified. >> >> Mark >> >> >> >>> On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren >>> <[email protected] <mailto:[email protected]>> wrote: >>> >>> Then something you have said isn’t right. In first email you >>> said that the pressure varies between -400 and +400 bar. Now >>> you say that the average can vary from -1000 to +1000 bar. If >>> the instantaneous pressure is varying from -1000 to +1000 bar, >>> then that is not a real issue. However, if the average can be >>> from -1000 to +1000 bar, then that definitely is. >>> >>> >>> Which one is it? >>> >>> >>> Catch ya, >>> >>> Dr. Dallas Warren >>> >>> Medicinal Chemistry and Drug Action >>> >>> Monash Institute of Pharmaceutical Sciences, Monash University >>> 381 Royal Parade, Parkville VIC 3010 >>> [email protected] <mailto:[email protected]> >>> >>> >>> +61 3 9903 9304 >>> --------------------------------- >>> When the only tool you own is a hammer, every problem begins >>> to resemble a nail. >>> >>> >>> *From:* [email protected] >>> <mailto:[email protected]> >>> [mailto:[email protected] >>> <mailto:[email protected]>] *On Behalf Of *Denny >>> Frost >>> *Sent:* Friday, 21 January 2011 9:23 AM >>> *To:* Discussion list for GROMACS users >>> *Subject:* Re: [gmx-users] Inaccurate pressure readings >>> >>> >>> The average I calculate is not within -10 to 10, it is on the >>> order of -1000 to 1000 >>> >>> On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren >>> <[email protected] <mailto:[email protected]>> >>> >>> wrote: >>> >>> You have a variable that is fluctuating over a range of 800+ >>> units (three orders of magnitude) and want the average to be 1.0? >>> >>> >>> It is not a problem as such. If you can get a large enough >>> data set of pressure data, and it will have to be very large, >>> then you might get it close to one. >>> >>> >>> But as long the average you calculate is within may be an >>> order of magnitude (-10 to 10) then there is nothing to get >>> too worried about. >>> >>> >>> Catch ya, >>> >>> Dr. Dallas Warren >>> >>> Medicinal Chemistry and Drug Action >>> >>> Monash Institute of Pharmaceutical Sciences, Monash University >>> 381 Royal Parade, Parkville VIC 3010 >>> [email protected] <mailto:[email protected]> >>> >>> >>> +61 3 9903 9304 >>> --------------------------------- >>> When the only tool you own is a hammer, every problem begins >>> to resemble a nail. >>> >>> >>> *From:* [email protected] >>> <mailto:[email protected]> >>> [mailto:[email protected] >>> <mailto:[email protected]>] *On Behalf Of *Denny >>> Frost >>> *Sent:* Friday, 21 January 2011 9:07 AM >>> *To:* [email protected] <mailto:[email protected]> >>> >>> *Subject:* [gmx-users] Inaccurate pressure readings >>> >>> >>> I am running a variety of NPT simulations with polar, >>> non-polar, and ionic compounds. Although my results for >>> density agree well with experimental values, the pressures I >>> get from g_energy are off by 1 to 3 orders of magnitude. In >>> the log file, the pressure fluctuates around a lot from -400 >>> to 400 bar, which seems to be normal according to other posts >>> on this list, but the average (which is what g_energy gives >>> me) is not 1.0 bar, as I specified. Does anyone know how to >>> correct this problem? >>> >>> >>> Pressure coupling parameters: >>> >>> Pcoupl = berendsen >>> >>> pcoupltype = isotropic >>> >>> tau_p = 1.0 >>> >>> ref_p = 1.0 >>> >>> compressibility = 4.5e-5 >>> >>> >>> -- >>> >>> >>> gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> >>> 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 [email protected] >>> <mailto:[email protected]>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> -- >>> gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> >>> 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 [email protected] >>> <mailto:[email protected]>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >> >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
