# How to solve :2 particles communicated to PME rank 1 are more than 2/3 times the cut-off out? **URL:** \ **Category:** User discussions\ **Created:** [April 11, 2024, 6:38am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847 "2024-04-11T06:38:17Z")\ **Posts on this page:** 8\ **Page:** 2
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [April 30, 2024, 4:42am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847/22 "2024-04-30T04:42:20Z")
Did you used the gro files that provides from ATB server? can you also share the topology file where you inserted all these itp. zip all the files and upload it in some file-sharing website (or gdrive) and share the link here. ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [April 30, 2024, 5:02am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847/23 "2024-04-30T05:02:35Z")
For example: You need to use the optimised geometry in the CCl4 topology: > **[Carbontetrachloride | CCl4 | MD Topology | NMR | X-Ray](https://atb.uq.edu.au/molecule.py?molid=3800#panel-md)** > > The Automated Topology Builder (ATB) and Repository is intended to facilitate the development of molecular force fields for Molecular Dynamics or Monte Carlo simulations of biomolecular systems. Applications include the study of biomolecule:ligand... ---
**Author:** ![aish.warya\_2024](https://avatars.discourse-cdn.com/v4/letter/a/b5ac83/32.png) [@aish.warya\_2024](https://gromacs.bioexcel.eu/u/aish.warya_2024)\ **Post date:** [April 30, 2024, 5:14am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847/25 "2024-04-30T05:14:36Z")
I have used original geometry all-atom pdb file of polymer downloaded from ATB and then converted it into gro using pdb2gmx command in gromacs. I will try with the optimised geometry also. I am attaching the zip file link: > **[Google Drive: Sign-in](https://accounts.google.com/v3/signin/identifier?continue=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11wV3NieZJgk6rEiaN1ilwq5ARJmZeHe1%2Fview%3Fusp%3Ddrive_link&followup=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11wV3NieZJgk6rEiaN1ilwq5ARJmZeHe1%2Fview%3Fusp%3Ddrive_link&ifkv=AaSxoQxaSsw6sayIfjATZdSeHtponubMYh5vDUimhL7hXsF_FTyvPH1mOf5VnFlyDRP-ZCvc0VJ_&osid=1&passive=1209600&service=wise&flowName=GlifWebSignIn&flowEntry=ServiceLogin&dsh=S168073493%3A1714453788246523&theme=mn&ddm=0)** > > Access Google Drive with a Google account (for personal use) or Google Workspace account (for business use). Thanks in advance ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [April 30, 2024, 5:28am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847/26 "2024-04-30T05:28:00Z")
You should use optimised geometry , it will work! ---
**Author:** ![aish.warya\_2024](https://avatars.discourse-cdn.com/v4/letter/a/b5ac83/32.png) [@aish.warya\_2024](https://gromacs.bioexcel.eu/u/aish.warya_2024)\ **Post date:** [April 30, 2024, 5:35am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847/27 "2024-04-30T05:35:54Z")
Thank you for your assistance. May I ask one more question? There are two optimized PDB files in ATB: allatom\_optimized\_geometry and unitedatom\_optimized\_geometry. Which geometry should I utilize ? ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [April 30, 2024, 1:11pm UTC](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847/28 "2024-04-30T13:11:16Z")
all atom would be better. ---
**Author:** ![aish.warya\_2024](https://avatars.discourse-cdn.com/v4/letter/a/b5ac83/32.png) [@aish.warya\_2024](https://gromacs.bioexcel.eu/u/aish.warya_2024)\ **Post date:** [April 30, 2024, 4:24pm UTC](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847/29 "2024-04-30T16:24:40Z")
Thank you. I will try this ---
**Author:** ![aish.warya\_2024](https://avatars.discourse-cdn.com/v4/letter/a/b5ac83/32.png) [@aish.warya\_2024](https://gromacs.bioexcel.eu/u/aish.warya_2024)\ **Post date:** [May 5, 2024, 4:28pm UTC](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847/30 "2024-05-05T16:28:16Z")
Dear @scinikhil, Thank you for your assistance. I have successfully equilibrated the system using NPT conditions and have now begun running the MD simulation. However, I now intend to model a water-chloroform interface with some polymer chains. How can I calculate the number of atoms and the size of the simulation box by knowing the density for the MD simulation? Your guidance in resolving this issue would be greatly appreciated. Additionally, could you provide some references for modeling a simulation box? Thank you once again. [Previous page](https://gromacs.bioexcel.eu/t/how-to-solve-2-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out/8847.md?page=1)