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

[David van der Spoel]

On 11/09/16 19:51, Faust SHI wrote:
> 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?
>
>
If there is nothing in th elog file please copy the entire error message 
from the console or your queue output file to the mail.
There should be something in your log file as well about the extent of 
interactions.

You may have to set the -dd flag to obtain more cubic boxes, for 24 
cores -dd 4 3 2 might work better.



> 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