乙醇与水摩尔比1:2混合体系的模拟问题

casperyue

在重复培训教程乙醇与水摩尔比1:2混合体系的模拟案例时，用chem3D构建乙醇和水的pdb文件，然后用两次gmx insert-molecules 命令构建混合体系生成mix.pdb文件，后续按教程步骤修改ethanol.itp文件，建立mix.top文件，进行能量极小化和平衡相MD,然后就在平衡相MD的计算中卡住进行不下去了。请问老师，是什么地方出问题了呢？

具体过程、文件及报错信息如下：

gmx insert-molecules -box 3 3 3 -ciethanol.pdb -nmol 150 -o temp.pdb

gmx insert-molecules -f temp.pdb -ciwater.pdb -nmol 300 -o mix.pdb

gmx grompp -f em.mdp -c mix.pdb -p mix.top-o em.tpr -maxwarn 1

获得em.tpr文件，被忽略的报错信息为：

Warning: atom name 1 in mix.top and mix.pdb does not match (OW - C)

Warning: atom name 2 in mix.top and mix.pdb does not match (HW1 - C)

Warning: atom name 3 in mix.top and mix.pdb does not match (HW2 - O)

Warning: atom name 4 in mix.top and mix.pdb does not match (OW - H)

Warning: atom name 5 in mix.top and mix.pdb does not match (HW1 - H)

Warning: atom name 6 in mix.top and mix.pdb does not match (HW2 - H)

Warning: atom name 7 in mix.top and mix.pdb does not match (OW - H)

Warning: atom name 8 in mix.top and mix.pdb does not match (HW1 - H)

Warning: atom name 9 in mix.top and mix.pdb does not match (HW2 - H)

Warning: atom name 10 in mix.top and mix.pdb does not match (OW - C)

Warning: atom name 11 in mix.top and mix.pdb does not match (HW1 -C)

Warning: atom name 12 in mix.top and mix.pdb does not match (HW2 -O)

Warning: atom name 13 in mix.top and mix.pdb does not match (OW - H)

Warning: atom name 14 in mix.top and mix.pdb does not match (HW1 -H)

Warning: atom name 15 in mix.top and mix.pdb does not match (HW2 -H)

Warning: atom name 16 in mix.top and mix.pdb does not match (OW - H)

Warning: atom name 17 in mix.top and mix.pdb does not match (HW1 -H)

Warning: atom name 18 in mix.top and mix.pdb does not match (HW2 -H)

Warning: atom name 19 in mix.top and mix.pdb does not match (OW - C)

Warning: atom name 20 in mix.top and mix.pdb does not match (HW1 -C)

(more than 20 non-matching atom names)

WARNING 1 [file mix.top, line 12]:

  2250 non-matching atom names

  atom names from mix.top willbe used

  atom names from mix.pdb willbe ignored

继续进行能量最小化并进行平衡相MD：

gmx mdrun -v -deffnm em

gmx grompp -f eq.mdp -c em.gro -p mix.top-o eq.tpr

gmx mdrun -v -deffnm eq

无法完成计算，报错信息如下：

step 0: One or more water molecules can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#

Wrote pdb files with previous and current coordinates

step 0Warning: Only triclinic boxes with the first vector parallelto the x-axis and the second vector in the xy-plane are supported.

         Box (3x3):

            Box[    0]={  -nan(ind),    -nan(ind),    -nan(ind)}

            Box[    1]={  -nan(ind),    -nan(ind),    -nan(ind)}

            Box[    2]={  -nan(ind),    -nan(ind),    -nan(ind)}

         Can not fix pbc.

casperyue

重复检查调试了10遍，终于发现漏掉一个信息。mix.top文件中的顺序需与mix.pdb中的一致。我是先插入的乙醇再插入的水。导致两者不一致了。现在已经可以继续计算下去。

sobereva

Warning: atom name 1 in mix.top and mix.pdb does not match (OW - C)
Warning: atom name 2 in mix.top and mix.pdb does not match (HW1 - C)
Warning: atom name 3 in mix.top and mix.pdb does not match (HW2 - O)
从warning一开始就明显知道结构文件和拓扑文件不对应，元素都对不上