[gmx-users] Regargding simulation of periodic silica surface

[Sathish Kumar]

So in SiO2 structure atoms are getting merged, is that the reason for the
error in simulation?

On Fri, Sep 12, 2014 at 6:57 AM, Mirco Wahab <
mirco.wahab at chemie.tu-freiberg.de> wrote:

> On 12.09.2014 13:30, Sathish Kumar wrote:
>
>> And here i attached the md.log file and em.gro file. Please once check.
>>
>
> I did run the SiO2 block of your .gro file through my distance
> checker and it looks like you have massive overlap through
> the y PBC boundary and one positional duplication:
>
>  1709 (Si)      ...  6358 (BO)  0          nm |     <-- two coordinates at
> the same location?
>
>   363 (Si)      ...  7007 (BO)  0.0222935  nm |    Y
>  2846 (BO)      ...  6875 (Si)  0.0286182  nm |    Y
>   396 (Si)      ...  7251 (BO)  0.0353554  nm |    Y
>   345 (Si)      ...  6971 (BO)  0.0362906  nm |    Y
>  2939 (BO)      ...  7018 (Si)  0.0476342  nm |    Y
>   344 (Si)      ...  6967 (BO)  0.055687   nm |    Y
>  1625 (Si)      ...  5439 (BO)  0.0573586  nm |    Y
>  1643 (Si)      ...  5449 (BO)  0.0588729  nm |    Y
>  2183 (Si)      ...  6404 (BO)  0.0593127  nm |    Y
>  1590 (Si)      ...  4186 (BO)  0.059716   nm |    Y
>  1608 (Si)      ...  4197 (BO)  0.0598749  nm |    Y
>   395 (Si)      ...  3077 (BO)  0.0683738  nm |    Y
>   362 (Si)      ...  7003 (BO)  0.0699715  nm |    Y
>  1001 (Si)      ...  4257 (BO)  0.0706683  nm |    Y
>  1019 (Si)      ...  4269 (BO)  0.0718127  nm |    Y
>   377 (Si)      ...  3065 (BO)  0.0724502  nm |    Y
>  2155 (Si)      ...  5378 (BO)  0.0726498  nm |    Y
>  2199 (Si)      ...  5448 (BO)  0.0736275  nm |    Y
>  2184 (Si)      ...  5438 (BO)  0.0739799  nm |    Y
>  2168 (Si)      ...  5387 (BO)  0.0742159  nm |    Y
>  1002 (Si)      ...  3064 (BO)  0.0759077  nm |    Y
>   397 (Si)      ...  7255 (BO)  0.0764789  nm |    Y
>  1020 (Si)      ...  3076 (BO)  0.0772658  nm |    Y
>  2876 (BO)      ...  6891 (Si)  0.0774145  nm |    Y
>  2845 (BO)      ...  6871 (Si)  0.078256   nm |    Y
>  2154 (Si)      ...  5376 (BO)  0.0801125  nm |    Y
>  2153 (Si)      ...  6402 (BO)  0.0808642  nm |    Y
>   379 (Si)      ...  7215 (BO)  0.0815047  nm |    Y
>  2167 (Si)      ...  5385 (BO)  0.0821037  nm |    Y
>  2185 (Si)      ...  5440 (BO)  0.0836657  nm |    Y
>  2200 (Si)      ...  5450 (BO)  0.0867524  nm |    Y
>  2875 (BO)      ...  6887 (Si)  0.0878234  nm |    Y
>   343 (Si)      ...  2995 (BO)  0.087972   nm |    Y
>   361 (Si)      ...  3006 (BO)  0.0882612  nm |    Y
>  2938 (BO)      ...  7014 (Si)  0.0884814  nm |    Y
>   378 (Si)      ...  7211 (BO)  0.0908792  nm |    Y
>  1003 (Si)      ...  3066 (BO)  0.0917607  nm |    Y
>   985 (Si)      ...  3007 (BO)  0.0943716  nm |    Y
>  1021 (Si)      ...  3078 (BO)  0.0945146  nm |    Y
>   967 (Si)      ...  2996 (BO)  0.0953992  nm |    Y
>
> (The atom id's are 0-based)
>
>
> Regards
>
> M.
>
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-- 
regards
M.SathishKumar