[gmx-users] Reg. mdrun error: not all ion group molecules consist of 3 atoms

Kutzner, Carsten ckutzne at gwdg.de
Fri Mar 16 11:15:03 CET 2018


> On 16. Mar 2018, at 02:39, 가디 장데부 고라크스나트 <f07338 at kist.re.kr> wrote:
> Hello,I am performing computational Electrophysiology gromacs tutorial.  I successfully pass the grompp for the compEL but failed with a Fatal error at mdrun step, not all ion group molecules consist of 3 atoms.my command for grompp was gmx_mpi_d grompp -f step7-prod.mdp -o step7-prod.tpr -c step6.6-double-box-in-Z.gro -n index-for-twin.ndx -p topol.top -maxwarn -1 , it runs successfully but when I tried with gmx_mpi_d mdrun -deffnm step7_prod it terminated with a fatal error.I did create an index group for TIP3|SOD|CLA together and named as SOL_ions and put inside step7_prod.mdp These are my .mdp file options tcoupl = Nose-Hoover, tc_groups = PROA PROB DMPC SOL_ions, tau_t = 1.0 1.0 1.0 1.0 , ref_t = 320.15 320.15 320.15 320.15, comm_grps = PROA PROB DMPC SOL_ions, rest of the parameters are default as like normal mdp file. Inside CompEL, swap-group = SOD, solvent-group = TIP3,Do I need to separate the coupling group SOL_ions, as TIP3,
From the name of the options I guess you are using GROMACS 5. For this version you should put
the ions that are under the control of the CompEL protocol into the swap-group. So this group can
contain sodium and chloride ions, but must not contain solvent molecules. The solvent molecules
(and no other atoms) must be in the solvent-group.

If you upgrade to GROMACS 2016 or later, there are more .mdp options giving you more control
about the groups (2016+ needs each ion type in a separate group, and you can have
as many as you like). But it should also work with the GROMACS 5 version that you are using.


>  SOD, CLA because in compEL I am going to swap between SOD and TIP3.Looking forward to hearing from you.Regards,ChangdevDr. Changdev G. GadhePost-Doc Researcher,Convergence Research Center for Diagnosis, Treatment and Care System of Dementia,Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850Email: F07338 at kist.re.kr
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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