Hi Berk, the tabulated potential I used (the file table_b.xvg) is exactly the function V(R)=1/2 *k*(R-R0)^2 in numerical form. I printed in the first column the R variable from 0 to 2 nm in step of 0.001 nm, on the second column the associated V(R) value (KJ/mol) and in the third column its derivatives. With this choice I chose the force constant k (that must be defined for tabulated function) to 1.0. About this point (please forgive me...it's probably a silly question!) I am a bit confused about this force constant since I don't understand its meaning... my numerical potential should be already correct in dimensions and units and so I guessed that k should have been equal to 1.0. Further, I use the occasion to ask you also if the x points in the table "should be uniformly spaced" as reported in the manual so that there are no problems even if it's not so or they "must be uniformly spaced" to obtain the correct results. Thank you,
AM ----Messaggio originale---- Da: [email protected] Data: 30-set-2009 1.36 PM A: <[email protected]>, "Discussion list for GROMACS users"<[email protected]> Ogg: RE: R: Re: R: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem --> Hi, Are you really sure you entered the tabulated potential correctly? There is for instance the pre-factor 1/2 in front of the harmonic potential, which you will have to add explicitly, either in the table or in the force constant. Berk Date: Wed, 30 Sep 2009 14:33:31 +0200 From: [email protected] To: [email protected] Subject: R: Re: R: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem Dear Mark, unfortunately the differences I was speaking about are very consistent. I am simulating a short chain with MARTINI CG force field: with an analytical harmonic potential the chain becomes a random coil, when using the same potential but in tabulated numerical form the chain remains extended and only slightly distorted from linearity. All the parameters of the simulation (box sizes, mdp option...) are the same. I will try the options for mdrun. Thank you, Alberto ----Messaggio originale---- Da: [email protected] Data: 30-set-2009 12.15 PM A: "Discussion list for GROMACS users"<[email protected]> Ogg: Re: R: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem [email protected] wrote: > I changed bond type to 8. > In any case the two MD simulations (same harmonic potential but in > analytical form vs tabulated form) gives different results. > All the pararameters of the simulation are the same. Slight differences will be normal unless you're running with "mdrun -reprod." Even then, there will be small differences between tabulated and non-tabulated. If you really want to be sure, you should consider doing an "mdrun -rerun -reprod" so that you are calculating the same quantities on the same inputs. Mark > ----Messaggio originale---- > Da: [email protected] > Data: 29-set-2009 3.54 PM > A: <[email protected]>, "Discussion list for GROMACS > users"<[email protected]> > Ogg: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem > > No. > > The ONLY difference between bonds type 8 and type 9 is that type 8 > generates exclusions > while type 9 does not (see table 5.4 in the manual). > Simply changing from type 9 to 8 will generate the exclusions. > > Berk > > ------------------------------------------------------------------------ > Date: Tue, 29 Sep 2009 17:52:03 +0200 > From: [email protected] > To: [email protected] > Subject: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem > > In my simulation I used bond type 9 because I was convinced that 1-2 LJ > interaction would have been excluded in any case as default for bond > stretching interaction. After my simulations it seems not and so I > suppose that I must use bond type 8 and list the exclusion in the > itp...Right? > > Alberto > > ----Messaggio originale---- > Da: [email protected] > Data: 29-set-2009 2.15 PM > A: "Discussion list for GROMACS users"<[email protected]> > Ogg: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem > > Are you really sure about this and that this is with bond type 8? > > The whole point of having a tabulated bond type 8 and 9 > is that 8 does generate exclusions and 9 does not. > > Berk > > ------------------------------------------------------------------------ > Date: Tue, 29 Sep 2009 14:17:37 +0200 > From: [email protected] > To: [email protected] > Subject: R: RE: R: RE: [gmx-users] Tabulated potential - Problem > > Hi, > > in order to check further which kind of problems are present when using > tabulated potential, I carried out two simulations on the same system by > using the same harmonic > potential for bond stretching but either in analytical form or in > tabulated form respectively. The > results of the two simulations are different! > I repeated the calculationis on just two bonded particles and I verified > that when using > analytical stretching potentials 1-2 LJ interactions are excluded while they > are not excluded when using tabulated potential. > Am I right? > > This should mean that I have to use a function type 8 and list > explicitly the elements of the [ > exclusions ] field or is there another method? > > Thanks > > Alberto > > ----Messaggio originale---- > Da: [email protected] > Data: 25-set-2009 12.27 PM > A: "Discussion list for GROMACS users"<[email protected]> > Ogg: RE: R: RE: [gmx-users] Tabulated potential - Problem > > Your system could be unstable. > You can check for large forces with mdrun -pforce > I don't know what a reasonable range of forces is, you can try 5000. > If you have instabilities, you should get large forces printed > before you get the fatal error. > > Berk > > > ------------------------------------------------------------------------ > Date: Fri, 25 Sep 2009 14:10:08 +0200 > From: [email protected] > To: [email protected] > Subject: R: RE: [gmx-users] Tabulated potential - Problem > > Unfortunately, my box sizes are not close to 23. I also carried out > calculations switching off PBC or on much smaller systems. > I received always the same error. > I tried also a geometry optimization. It finished without warnings nor > errors: anyway the potential energy changed only very slightly during > the simulation with too large values. > > Thanks > > AM > > ----Messaggio originale---- > Da: [email protected] > Data: 24-set-2009 11.29 AM > A: "Discussion list for GROMACS users"<[email protected]> > Ogg: RE: [gmx-users] Tabulated potential - Problem > > This is not nonsense, it is exactly what is says. > The distance between two atoms is more than 10 times as large as your > table length. > > Maybe you are somehow having issues with periodic boundary conditions. > Is you box size close to 23? > > Berk > > > ------------------------------------------------------------------------ > Date: Thu, 24 Sep 2009 12:32:36 +0200 > From: [email protected] > To: [email protected] > Subject: [gmx-users] Tabulated potential - Problem > > Hi, > > I'm trying to carry out a CG simulation and I'm using > a tabulated potential for a bond stretching term. > My MD simulations stops immediately with the error message: > > ------------------------------------------------------- > Program mdrun_mpi, VERSION 4.0.5 > Source code file: bondfree.c, line: 1772 > > Fatal error: > A tabulated bond interaction table number 0 is out of the table range: r > 23.678833, between table indices 12069 and 12070, table length 1020 > ------------------------------------------------------- > > This should mean that some distances are beyond table length (as > reported in the manual) but this is > nonsense considering my input files and topology. > > Do you have any suggestion? > Thanks! > > AM > > > ------------------------------------------------------------------------ > Express yourself instantly with MSN Messenger! MSN Messenger > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > > ------------------------------------------------------------------------ > What can you do with the new Windows Live? Find out > <http://www.microsoft.com/windows/windowslive/default.aspx> > > > ------------------------------------------------------------------------ > Express yourself instantly with MSN Messenger! MSN Messenger > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > > ------------------------------------------------------------------------ > Express yourself instantly with MSN Messenger! MSN Messenger > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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! > 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/mailing_lists/users.php _______________________________________________ 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? 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