Dear Mark, <br>unfortunately the differences I was speaking about are very consistent. <br>I am simulating a short chain with MARTINI CG force field: <br>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.<br>I will try the options for mdrun.<br>Thank you,<br><br>Alberto<br>
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----Messaggio originale----<br>Da: Mark.Abraham@anu.edu.au<br>Data: 30-set-2009 12.15 PM<br>A: "Discussion list for GROMACS users"<gmx-users@gromacs.org><br>Ogg: Re: R: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem<br><br>albitauro@virgilio.it wrote:<br>> I changed bond type to 8.<br>> In any case the two MD simulations (same harmonic potential but in <br>> analytical form vs tabulated form) gives different results.<br>> All the pararameters of the simulation are the same.<br><br>Slight differences will be normal unless you're running with "mdrun <br>-reprod." Even then, there will be small differences between tabulated <br>and non-tabulated. If you really want to be sure, you should consider <br>doing an "mdrun -rerun -reprod" so that you are calculating the same <br>quantities on the same inputs.<br><br>Mark<br><br>> ----Messaggio originale----<br>> Da: gmx3@hotmail.com<br>> Data: 29-set-2009 3.54 PM<br>> A: <albitauro@virgilio.it>, "Discussion list for GROMACS <br>> users"<gmx-users@gromacs.org><br>> Ogg: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem<br>> <br>> No.<br>> <br>> The ONLY difference between bonds type 8 and type 9 is that type 8 <br>> generates exclusions<br>> while type 9 does not (see table 5.4 in the manual).<br>> Simply changing from type 9 to 8 will generate the exclusions.<br>> <br>> Berk<br>> <br>> ------------------------------------------------------------------------<br>> Date: Tue, 29 Sep 2009 17:52:03 +0200<br>> From: albitauro@virgilio.it<br>> To: gmx-users@gromacs.org<br>> Subject: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem<br>> <br>> In my simulation I used bond type 9 because I was convinced that 1-2 LJ <br>> interaction would have been excluded in any case as default for bond <br>> stretching interaction. After my simulations it seems not and so I <br>> suppose that I must use bond type 8 and list the exclusion in the <br>> 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>> 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>> ------------------------------------------------------------------------<br>> 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 <br>> using the same harmonic<br>> potential for bond stretching but either in analytical form or in <br>> 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 <br>> 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 <br>> 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>> ------------------------------------------------------------------------<br>> 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 <br>> 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 <br>> errors: anyway the potential energy changed only very slightly during <br>> 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 <br>> 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>> ------------------------------------------------------------------------<br>> 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 <br>> 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 <br>> 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>> ------------------------------------------------------------------------<br>> Express yourself instantly with MSN Messenger! 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