Interesting... Does it also happen on the mu or only on the <mu>? I ask this because the <mu>, unlike the mu, has the volume in it (as per the Widom insertion equations for the isothermic-isobaric ensemble). If the "-inf" is only on the <mu>, I'd suggest checking the volume along the trajectory (using g_energy, for example, or check the .xvg file from the -tpi flag, which already has the volume, I think). Check the post-processed trajectory that you feed mdrun -rerun, as your trajectory-processing script for TPIC may be doing something strange to the box size.
I recognize that the single/double-precision is intriguing, if indeed the problem is the volume. João On Fri, Jun 13, 2014 at 11:10 PM, Rafael I. Silverman y de la Vega < rsilv...@ucsc.edu> wrote: > Hi João, > I dont think its an excessive number of unfavorable insertions. The mu > getting output with double precision are > Reading frame 40 time 1770.000 mu -6.570e+01 <mu> -7.654e+01 > Reading frame 50 time 1775.000 mu -4.985e+01 <mu> -7.609e+01 > Reading frame 60 time 1780.000 mu -7.010e+01 <mu> -7.571e+01 > Reading frame 70 time 1785.000 mu -5.669e+01 <mu> -7.540e+01 > Reading frame 80 time 1790.000 mu -4.749e+01 <mu> -7.511e+01 > Reading frame 90 time 1795.000 mu -7.355e+01 <mu> -7.590e+01 > > to give a fairly representative sample. So, no, they arent near 100, and > are negative... And the issue seems to happen with later insertions, not > the first few... One run I just did, only the very last average mu was > -inf, (not even the mu for that frame, just the average mu after that > frame) which really seems to imply some sort of overflow problem > > Reading frame 180 time 1790.000 mu -1.284e+02 <mu> -1.153e+02 > Reading frame 190 time 1795.000 mu -7.920e+01 <mu> -inf > (not the same run as above, this was run in single precision) > > > On Thu, Jun 12, 2014 at 7:06 AM, João M. Damas <jmda...@itqb.unl.pt> > wrote: > > > Hello Rafael, > > > > High energies (energy differences) are not discarded. When summing them > > through the exponential of their negative, they contribute very little to > > the final sum (lower energies dominate the sum). Hence, they are > > "discarded". > > > > The "-inf" value on the mu standard error output is normal because, > unlike > > the -tpi output, there is no ternary operator checking if the sum of > > exponentials is equal to zero (when it is, the log of zero gives you the > > inf value). > > > > The change to the double precision not giving you the "-inf" also makes > > sense, because the sum of exponentials, which on single-precision was > zero, > > can now be non-zero due to the higher number of decimal places on > > double-precision. I am guessing with double-precision you are getting > very > > high positive numbers (energies) for the mu, around 1000 maybe? > > > > My interpretation is that it is hard to find a "favorable place" to > insert > > the water molecule in that cavity, at least with a few frames. I am > > guessing that with more and more frames, that may change, which is > natural. > > > > I hope this has helped. > > > > Cheers, > > João > > > > > > > > On Thu, Jun 12, 2014 at 10:45 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 6/11/14, 8:55 PM, Rafael I. Silverman y de la Vega wrote: > > > > > >> I mistyped amber, when I should have typed charmm, amber is totally > > >> uninvolved in my calculations. I used the script from > > >> http://www.gromacs.org/Downloads/User_contributions/Other_software > > titled > > >> charmm2gromacs. The output looked fine after running it. > > >> > > >> And, I doubt its the cofactor, just ran the insertion with double > > >> precision mdrun, it gave reasonable looking results. There seems to be > > >> some > > >> sort of issue with unreasonable interaction energies not being > discarded > > >> properly. > > >> > > >> > > > It's entirely possible that there's something wrong with the tpic code; > > > you can certainly file a bug report on Redmine with input files to > > > reproduce it. > > > > > > > > > -Justin > > > > > > > > >> On Tue, Jun 10, 2014 at 3:41 PM, Justin Lemkul <jalem...@vt.edu> > wrote: > > >> > > >> > > >>> > > >>> On 6/10/14, 6:14 PM, Rafael I. Silverman y de la Vega wrote: > > >>> > > >>> I meant that I only changed to cofactor to gromacs chamm27 format, > not > > >>>> amber format. I used charmm27 for the apoprotein as well as the > > >>>> cofactor. > > >>>> > > >>>> > > >>>> What script did you use? I don't understand why Amber99SB is > > involved > > >>> here, so I don't know exactly what you were doing to create the > > topology. > > >>> It may not end up being useful information, but it's important to > > >>> establish the validity of the underlying physical model. > > >>> > > >>> > > >>> -Justin > > >>> > > >>> > > >>> On Tue, Jun 10, 2014 at 3:09 PM, Justin Lemkul <jalem...@vt.edu> > > wrote: > > >>>> > > >>>> > > >>>> > > >>>>> On 6/10/14, 6:04 PM, Rafael I. Silverman y de la Vega wrote: > > >>>>> > > >>>>> you think it was the cofactor model? > > >>>>> > > >>>>>> > > >>>>>> > > >>>>>> If you're using a CHARMM-parametrized cofactor with an Amber99SB > > >>>>>> > > >>>>> protein, > > >>>>> I'd say the simulations are wholly unreliable. It's certainly the > #1 > > >>>>> likely cause for nonsensical results. If you want to get to the > root > > >>>>> of > > >>>>> the issue, you need to start with a solid foundation. > > >>>>> > > >>>>> Unless that's not what your last message meant? When you say "only > > >>>>> changed the cofactor," that implied to me that you didn't > > consistently > > >>>>> convert everything in the system. > > >>>>> > > >>>>> > > >>>>> -Justin > > >>>>> > > >>>>> > > >>>>> On Tue, Jun 10, 2014 at 2:23 PM, Justin Lemkul <jalem...@vt.edu> > > >>>>> wrote: > > >>>>> > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>>> On 6/10/14, 5:01 PM, Rafael I. Silverman y de la Vega wrote: > > >>>>>>> > > >>>>>>> wait, I only changed the cofactor to gromacs charmm27.ff > format > > >>>>>>> > > >>>>>>> > > >>>>>>>> > > >>>>>>>> Pretty amazing that the simulation even ran with that mash-up > > of > > >>>>>>>> > > >>>>>>>> parameters :) > > >>>>>>> > > >>>>>>> I'd say that's the most likely cause of your problems; > nonsensical > > >>>>>>> physical model leads to nonsensical output. > > >>>>>>> > > >>>>>>> -Justin > > >>>>>>> > > >>>>>>> > > >>>>>>> > > >>>>>>> On Tue, Jun 10, 2014 at 1:58 PM, Rafael I. Silverman y de la > > Vega > > >>>>>>> < > > >>>>>>> > > >>>>>>> rsilv...@ucsc.edu> wrote: > > >>>>>>>> > > >>>>>>>> I suppose something might be wrong with the simulations. I > am > > >>>>>>>> using > > >>>>>>>> > > >>>>>>>> gromacs 4.6.5, I am simulating a protein with a cofactor, > > someone > > >>>>>>>> > > >>>>>>>>> else > > >>>>>>>>> parametrized it, I changed from charmm to gromacs amber99sb.ff > > >>>>>>>>> format > > >>>>>>>>> with > > >>>>>>>>> a script on the gromacs website. I did a typical em/nvt/npt > > >>>>>>>>> equilibration > > >>>>>>>>> followed by a 5 ns production run. I picked 250 frames out of > the > > >>>>>>>>> trajectory, and altered them to the TPIC input format with a > > >>>>>>>>> script I > > >>>>>>>>> wrote, to insert the particle half way between two atoms that I > > >>>>>>>>> chose. > > >>>>>>>>> I > > >>>>>>>>> am > > >>>>>>>>> inserting a water molecule. When I run the actual insertion > some > > of > > >>>>>>>>> the > > >>>>>>>>> frames have a reasonable looking mu, and some have -inf mu. I > > think > > >>>>>>>>> it > > >>>>>>>>> may > > >>>>>>>>> have to do with cavity size, some frames have too small of a > > >>>>>>>>> cavity, > > >>>>>>>>> so > > >>>>>>>>> the > > >>>>>>>>> interaction energy of the inserted water diverges... > > >>>>>>>>> > > >>>>>>>>> > > >>>>>>>>> On Mon, Jun 9, 2014 at 6:40 PM, Justin Lemkul <jalem...@vt.edu > > > > >>>>>>>>> wrote: > > >>>>>>>>> > > >>>>>>>>> > > >>>>>>>>> > > >>>>>>>>> On 6/9/14, 6:41 PM, Rafael I. Silverman y de la Vega wrote: > > >>>>>>>>> > > >>>>>>>>>> > > >>>>>>>>>> Hi all, I am having a problem with -inf mu coming out of > > TPIC > > >>>>>>>>>> > > >>>>>>>>>> calculations. > > >>>>>>>>>> > > >>>>>>>>>>> Anyone have some suggestions on how to avoid this? Tabulated > > >>>>>>>>>>> potentials? > > >>>>>>>>>>> Or > > >>>>>>>>>>> can I modify the source code to reject the absurd values that > > >>>>>>>>>>> cause > > >>>>>>>>>>> this? I > > >>>>>>>>>>> read a few old discussions on this, I didnt see much on how > to > > >>>>>>>>>>> handle > > >>>>>>>>>>> this. > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>>> I'd be much more concerned that something is going wrong > in > > >>>>>>>>>>> the > > >>>>>>>>>>> > > >>>>>>>>>>> simulations. I have no experience with TPIC, but if you > post > > >>>>>>>>>>> more > > >>>>>>>>>>> > > >>>>>>>>>> detailed > > >>>>>>>>>> information about what you're doing and which Gromacs version > > >>>>>>>>>> you're > > >>>>>>>>>> using, > > >>>>>>>>>> you're more likely to get some suggestions. > > >>>>>>>>>> > > >>>>>>>>>> -Justin > > >>>>>>>>>> > > >>>>>>>>>> -- > > >>>>>>>>>> ================================================== > > >>>>>>>>>> > > >>>>>>>>>> Justin A. Lemkul, Ph.D. > > >>>>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow > > >>>>>>>>>> > > >>>>>>>>>> Department of Pharmaceutical Sciences > > >>>>>>>>>> School of Pharmacy > > >>>>>>>>>> Health Sciences Facility II, Room 601 > > >>>>>>>>>> University of Maryland, Baltimore > > >>>>>>>>>> 20 Penn St. > > >>>>>>>>>> Baltimore, MD 21201 > > >>>>>>>>>> > > >>>>>>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > >>>>>>>>>> http://mackerell.umaryland.edu/~jalemkul > > >>>>>>>>>> > > >>>>>>>>>> ================================================== > > >>>>>>>>>> -- > > >>>>>>>>>> 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 gmx-users-requ...@gromacs.org. > > >>>>>>>>>> > > >>>>>>>>>> > > >>>>>>>>>> > > >>>>>>>>>> > > >>>>>>>>>> -- > > >>>>>>>>> > > >>>>>>>>> ================================================== > > >>>>>>>> > > >>>>>>> > > >>>>>>> Justin A. Lemkul, Ph.D. > > >>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow > > >>>>>>> > > >>>>>>> Department of Pharmaceutical Sciences > > >>>>>>> School of Pharmacy > > >>>>>>> Health Sciences Facility II, Room 601 > > >>>>>>> University of Maryland, Baltimore > > >>>>>>> 20 Penn St. > > >>>>>>> Baltimore, MD 21201 > > >>>>>>> > > >>>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > >>>>>>> http://mackerell.umaryland.edu/~jalemkul > > >>>>>>> > > >>>>>>> ================================================== > > >>>>>>> -- > > >>>>>>> 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 gmx-users-requ...@gromacs.org. > > >>>>>>> > > >>>>>>> > > >>>>>>> -- > > >>>>>>> > > >>>>>> ================================================== > > >>>>> > > >>>>> Justin A. Lemkul, Ph.D. > > >>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow > > >>>>> > > >>>>> Department of Pharmaceutical Sciences > > >>>>> School of Pharmacy > > >>>>> Health Sciences Facility II, Room 601 > > >>>>> University of Maryland, Baltimore > > >>>>> 20 Penn St. > > >>>>> Baltimore, MD 21201 > > >>>>> > > >>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > >>>>> http://mackerell.umaryland.edu/~jalemkul > > >>>>> > > >>>>> ================================================== > > >>>>> -- > > >>>>> 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 gmx-users-requ...@gromacs.org. > > >>>>> > > >>>>> > > >>>>> -- > > >>> ================================================== > > >>> > > >>> Justin A. Lemkul, Ph.D. > > >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow > > >>> > > >>> Department of Pharmaceutical Sciences > > >>> School of Pharmacy > > >>> Health Sciences Facility II, Room 601 > > >>> University of Maryland, Baltimore > > >>> 20 Penn St. > > >>> Baltimore, MD 21201 > > >>> > > >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > >>> http://mackerell.umaryland.edu/~jalemkul > > >>> > > >>> ================================================== > > >>> -- > > >>> 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 gmx-users-requ...@gromacs.org. > > >>> > > >>> > > > -- > > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > > > Department of Pharmaceutical Sciences > > > School of Pharmacy > > > Health Sciences Facility II, Room 601 > > > University of Maryland, Baltimore > > > 20 Penn St. > > > Baltimore, MD 21201 > > > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > http://mackerell.umaryland.edu/~jalemkul > > > > > > ================================================== > > > -- > > > 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 gmx-users-requ...@gromacs.org. > > > > > > > > > > > -- > > João M. Damas > > PhD Student > > Protein Modelling Group > > ITQB-UNL, Oeiras, Portugal > > Tel:+351-214469613 > > -- > > 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 gmx-users-requ...@gromacs.org. > > > -- > 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 gmx-users-requ...@gromacs.org. > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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 gmx-users-requ...@gromacs.org.