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wjf12銀蟲 (小有名氣)
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[求助]
Gromacs能量最小化問題 已有1人參與
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有請高人指點！��！ 我運行的是CaO8個晶胞的能量最小化，以下是運行g(shù)romacs是遇到的問題： NOTE 1 [file CaO8.top, line 24]: System has non-zero total charge: 2.000000e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Making dummy/rest group for Acceleration containing 125 elements Making dummy/rest group for Freeze containing 125 elements Making dummy/rest group for Energy Mon. containing 125 elements Making dummy/rest group for VCM containing 125 elements Number of degrees of freedom in T-Coupling group System is 372.00 Making dummy/rest group for User1 containing 125 elements Making dummy/rest group for User2 containing 125 elements Making dummy/rest group for XTC containing 125 elements Making dummy/rest group for Or. Res. Fit containing 125 elements Making dummy/rest group for QMMM containing 125 elements T-Coupling has 1 element(s): System Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 36x36x36, spacing 0.222 0.222 0.222 Estimate for the relative computational load of the PME mesh part: 0.86 NOTE 2 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 0 Mb of data writing run input file... [ Last edited by wjf12 on 2014-3-11 at 16:41 ] |
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wjf12
銀蟲 (小有名氣)
- 應(yīng)助: 0 (幼兒園)
- 金幣: 300.6
- 帖子: 78
- 在線: 48.5小時
- 蟲號: 2476378
- 注冊: 2013-05-22
- 專業(yè): 工程熱物理相關(guān)交叉領(lǐng)域
3樓2014-03-11 19:02:22
2樓2014-03-11 17:03:10
wjf12
銀蟲 (小有名氣)
- 應(yīng)助: 0 (幼兒園)
- 金幣: 300.6
- 帖子: 78
- 在線: 48.5小時
- 蟲號: 2476378
- 注冊: 2013-05-22
- 專業(yè): 工程熱物理相關(guān)交叉領(lǐng)域
4樓2014-03-14 20:09:44
5樓2014-03-16 20:14:59
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