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?<BR><BR>Alberto <BR><BR>----Messaggio originale----<BR>Da: gmx3@hotmail.com<BR>Data: 29-set-2009 2.15 PM<BR>A: "Discussion list for GROMACS users"<gmx-users@gromacs.org><BR>Ogg: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem<BR><BR><!--
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-->Are you really sure about this and that this is with bond type 8?<BR><BR>The whole point of having a tabulated bond type 8 and 9<BR>is that 8 does generate exclusions and 9 does not.<BR><BR>Berk<BR><BR>
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Date: Tue, 29 Sep 2009 14:17:37 +0200<BR>From: albitauro@virgilio.it<BR>To: gmx-users@gromacs.org<BR>Subject: R: RE: R: RE: [gmx-users] Tabulated potential - Problem<BR><BR>Hi,<BR><BR>in order to check further which kind of problems are present when using<BR>tabulated potential, I carried out two simulations on the same system by using the same harmonic<BR>potential for bond stretching but either in analytical form or in tabulated form respectively. The<BR>results of the two simulations are different!<BR>I repeated the calculationis on just two bonded particles and I verified that when using<BR>analytical stretching potentials 1-2 LJ interactions are excluded while they<BR>are not excluded when using tabulated potential.<BR>Am I right?<BR><BR>This should mean that I have to use a function type 8 and list explicitly the elements of the [<BR>exclusions ] field or is there another method?<BR><BR>Thanks<BR><BR>Alberto<BR><BR>----Messaggio originale----<BR>Da: gmx3@hotmail.com<BR>Data: 25-set-2009 12.27 PM<BR>A: "Discussion list for GROMACS users"<gmx-users@gromacs.org><BR>Ogg: RE: R: RE: [gmx-users] Tabulated potential - Problem<BR><BR>Your system could be unstable.<BR>You can check for large forces with mdrun -pforce<BR>I don't know what a reasonable range of forces is, you can try 5000.<BR>If you have instabilities, you should get large forces printed<BR>before you get the fatal error.<BR><BR>Berk<BR><BR><BR>
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Date: Fri, 25 Sep 2009 14:10:08 +0200<BR>From: albitauro@virgilio.it<BR>To: gmx-users@gromacs.org<BR>Subject: R: RE: [gmx-users] Tabulated potential - Problem<BR><BR>Unfortunately, my box sizes are not close to 23. I also carried out calculations switching off PBC or on much smaller systems. <BR>I received always the same error. <BR>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.<BR><BR>Thanks<BR><BR>AM<BR><BR>----Messaggio originale----<BR>Da: gmx3@hotmail.com<BR>Data: 24-set-2009 11.29 AM<BR>A: "Discussion list for GROMACS users"<gmx-users@gromacs.org><BR>Ogg: RE: [gmx-users] Tabulated potential - Problem<BR><BR>This is not nonsense, it is exactly what is says.<BR>The distance between two atoms is more than 10 times as large as your table length.<BR><BR>Maybe you are somehow having issues with periodic boundary conditions.<BR>Is you box size close to 23?<BR><BR>Berk<BR><BR><BR>
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Date: Thu, 24 Sep 2009 12:32:36 +0200<BR>From: albitauro@virgilio.it<BR>To: gmx-users@gromacs.org<BR>Subject: [gmx-users] Tabulated potential - Problem<BR><BR>Hi,<BR><BR>I'm trying to carry out a CG simulation and I'm using<BR>a tabulated potential for a bond stretching term.<BR>My MD simulations stops immediately with the error message:<BR><BR>-------------------------------------------------------<BR>Program mdrun_mpi, VERSION 4.0.5<BR>Source code file: bondfree.c, line: 1772<BR><BR>Fatal error:<BR>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<BR>-------------------------------------------------------<BR><BR>This should mean that some distances are beyond table length (as reported in the manual) but this is<BR>nonsense considering my input files and topology.<BR><BR>Do you have any suggestion?<BR>Thanks!<BR><BR>AM<BR><BR><BR>
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