[gmx-users] Initial cell size is smaller than the cell size

Faust SHI shi86 at wisc.edu
Sun Sep 11 19:51:26 CEST 2016

Date: Sat, 10 Sep 2016 21:42:37 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Initial cell size is smaller than the cell
        size    limit
Message-ID: <b65e2a23-2f0f-13fb-12e9-e31373fd6e5b at xray.bmc.uu.se>
Content-Type: text/plain; charset=gbk; format=flowed

On 10/09/16 19:56, Faust SHI wrote:
> Hi Sir,
> When I just run my simulation after I use grompp to convert tpr file, the error occurs that "Fatal error: The initial cell size (4.180000) is smaller than the cell size limit (11.011738), change options -dd, -rdd or -rcon, see the log file for details?. Do you have any idea about what causes this error or what controls the cell size limit so that I can make it match the initial cell size?
> Thanks a lot!
Depends on cut-off, system details like shape of the box, whether you
have periodic molecules etc. Please also copy-paste the entire error
message from your md.log file.

> Yours sincerely,
> Faust

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se<http://folding.bmc.uu.se/>

Hi David,

Thanks for your reply!

Actually there is no any error message  in md.log file except "

Number of logical cores detected (24) does not match the number reported by OpenMP (12). Consider setting the launch configuration manually!

Running on 2 nodes with total 24 cores, 48 logical cores

  Cores per node:           12

  Logical cores per node:   24

Hardware detected on host compute-0-19.local (the node of MPI rank 0):

  CPU info:

    Vendor: GenuineIntel

    Brand:  Intel(R) Xeon(R) CPU E5-2620 0 @ 2.00GHz

    Family:  6  model: 45  stepping:  7

    CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic

    SIMD instructions most likely to fit this hardware: AVX_256

    SIMD instructions selected at GROMACS compile time: AVX_256",

which is also in error message file from the cluster. Is this the reason making a small initial cell size or large cell size limit? How to fix it?

Yours sincerely,


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