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.
AM ----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 What can you do with the new Windows Live? Find out Express yourself instantly with MSN Messenger! MSN Messenger Express yourself instantly with MSN Messenger! MSN Messenger
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