Justin, unfortunately my last system have also been crashed after 35ns of simulation with the links warnings accompanied by the error
Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This time I've devided all functional groups of my ADENOSINE ligand into separate charge groups in topol.itp. ; nr type resnr resid atom cgnr charge mass total_charge 1 NT 1 ADN N6 1 -0.844 14.0067 2 H 1 ADN H11 1 0.422 1.0080 3 H 1 ADN H12 1 0.422 1.0080 ; 0.000 4 C 1 ADN C8 2 0.097 12.0110 5 HC 1 ADN H01 2 0.177 1.0080 6 NR 1 ADN N3 2 -0.642 14.0067 7 C 1 ADN C4 2 0.175 12.0110 8 C 1 ADN C5 2 0.092 12.0110 9 NR 1 ADN N7 2 -0.556 14.0067 10 C 1 ADN C6 2 0.657 12.0110 ; 0.000 11 C 1 ADN C5' 3 -0.677 12.0110 12 C 1 ADN C4' 3 0.834 12.0110 13 OE 1 ADN O4' 3 -0.248 15.9994 14 C 1 ADN C1' 3 -0.558 12.0110 15 C 1 ADN C2' 4 0.603 12.0110 16 C 1 ADN C3' 5 -0.212 12.0110 17 NR 1 ADN N9 3 0.415 14.0067 18 OA 1 ADN O2' 4 -0.606 15.9994 19 H 1 ADN H08 4 0.482 1.0080 20 OA 1 ADN O3' 5 -0.606 15.9994 21 H 1 ADN H06 5 0.482 1.0080 22 OA 1 ADN O5' 3 -0.246 15.9994 23 H 1 ADN H03 3 0.337 1.0080 ; -0.000 24 C 1 ADN C2 6 0.502 12.0110 25 HC 1 ADN H10 6 0.106 1.0080 26 NR 1 ADN N1 6 -0.608 14.0067 ; 0.000 Also I've done proper equilibration in tho steps (I've used 1fs integrator steps on both stages of equilibration) 1- I've made equilibration with posres ( 500ps) on protein backbone atoms as well as ligand with x-ray water 2- The next step (5ns) was done without posres only with smaller integrator steps. What another possible sollutions could be ? James 2012/7/7, Justin A. Lemkul <jalem...@vt.edu>: > > > On 7/7/12 11:08 AM, James Starlight wrote: >> justin, >> >> It seems that problem was in the big charge groups in the ligand.itp >> file. In particularly I've devided largest group into several smaller >> and there haven't any crashes been occured yet. >> >> With my last system with the the default COM group I've obtained crash >> on the 25ns with the error about ligand's big cngr exactly. >> >> >> By the way could you tell me how I could analyse stability of the >> protein-ligand system as well as contributions of the individual >> non-covalent contacts with the .EDR file? >> >> In my mdp file I've defined energygrps= Protein Ligand as the >> separate energy terms. >> >> During analysis of the edr file I've observed some options like >> LJ-SR:Protein-ADN ( this value was slightly negative (-100) during my >> trr ) >> Coul-14:Protein-ADN ( this value was constantly zero ) >> Coul-SR:ADN-rest ( this value was equal to the LJ-SR:Protein-ADN -100 ) >> >> What conclusions in general could I do based on that values ? How I >> could measure stability of the ligand ( beside dirrect RMSD >> measurement) from such energy terms? >> > > In isolation, these values are not indicative of anything. Their absolute > values are completely dependent upon the parameters set in the topology. > Force > field parameterization methodology does not require that any topology > reproduce > protein-ligand energetics; only true free energy calculations might tell you > this. > > In conjunction with other metrics (hydrogen bonding, contacts, RMSD, SASA, > etc) > you may be able to make some meaningful observations about ligand stability > in > the protein binding site. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
