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标题: [已解决]使用packmol建立的模型，在mdrun的时候，因能量太大而无法继续 [打印本页]

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Author: 牧生 时间: 2021-1-24 17:06
标题: [已解决]使用packmol建立的模型，在mdrun的时候，因能量太大而无法继续
本帖最后由牧生于 2021-1-25 16:34 编辑

使用讲义中的水和尿素两相体系进行md过程，是没有报错的，证明我的操作基本是行得通的。

自己使用表面活性剂，如CTAB以insert-molecules的方式向盒子中加入分子，再进行MD，整个过程是行得通的，结果中也观察得到了球形胶束。。

但自己进行表面活性剂，使用packmol建模后进行操作，就出现了错误。具体如下：

① 以MS画出了CTAB的分子式，存为pdb格式，

② 上传http://bio2byte.be/acpype/，手动设为电荷为1，获得top，gro，itp文件

③ 将MS得到的CTAB.pdb，使用packmol建立一个圆柱状的模型，其中CTAB不是很致密，

tolerance 2.0

add_box_sides 1.2

output mix.pdb

structure CTAB.pdb

number 100

inside cylinder 0. 0. 0. 100. 0. 0. 30. 100.

end structure

得到圆柱的pdb文件如图所示，

(, 下载次数 Times of downloads: 51)

④ 加入水

gmx solvate -cp mix.pdb -cs tip4p.gro -p CTAB_GMX.top -o CTAB_solv.gro

修改top文件中的CTAB为100

引入力场

#include "oplsaa.ff/forcefield.itp"

#include "CTAB_GMX.itp"

#include "oplsaa.ff/tip4p.itp"

⑤能量最小 #初步觉得能量最小这一步有问题，但是看起来，自己又看不出问题

define =

integrator = steep

emtol = 100.0

emstep = 0.01

nsteps = 10000

; output frequency

nstxout = 5000

nstvout = 5000

nstfout = 5000

nstlog = 5000

nstenergy = 5000

nstxtcout =5000

xtc_grps = system

nstlist = 10

pbc = xyz

rlist = 1.2

cutoff-scheme = Verlet

coulombtype = PME

rcoulomb = 1.2

vdwtype = cut-off

rvdw = 1.2

DispCorr = EnerPres

constraints = none

constraint_algorithm = LINCS

implicit_solvent = no

E_x =

E_y =

E_z =

gmx grompp -f em.mdp -c CTAB_solv.gro -p CTAB_GMX.top -o CTAB.tpr -maxwarn 2

gmx mdrun -deffnm CTAB -v

⑥加入离子，使电荷平衡

gmx genion -s CTAB.tpr -o CTAB-b4em.gro -neutral -p CTAB_GMX.top

再向top里面加入

#include "oplsaa.ff/ions.itp"

再进行能量最小

gmx grompp -f em.mdp -c CTAB-b4em.gro -p CTAB_GMX.top -o em-sol.tpr

gmx mdrun -deffnm em-sol –v

得到potential

(, 下载次数 Times of downloads: 33)

⑦ 进行nvt预平衡

;define=

cutoff-scheme= Verlet

integrator= md

dt = 0.001

nsteps = 50000

nstxout= 500

nstvout= 500

nstenergy= 500

nstlog= 500

energygrps =system

nstlist= 10

ns_type = grid

pbc= xyz

rlist= 1.0

coulombtype= PME

pme_order= 4

fourierspacing= 0.16

rcoulomb= 1.0

vdw-type= Cut-off

rvdw= 1.0

tcoupl = v-rescale

tc-grps= system

tau_t= 0.1

ref_t= 300

DispCorr= EnerPres

pcoupl = no

gen_vel = no

gen_temp = 300

gen_seed = -1

constraints = hbonds

continuation= no

constraint_algorithm= lincs

lincs_iter = 1

lincs_order= 4

出现错误

Step 0, time 0 (ps) LINCS WARNING

relative constraint deviation after LINCS:

rms 0.080675, max 3.668313 (between atoms 8436 and 8461)

bonds that rotated more than 30 degrees:

atom 1 atom 2 angle previous, current, constraint length

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

starting mdrun 'CTABMS in water'

50000 steps, 50.0 ps.

WARNING: Listed nonbonded interaction between particles 8314 and 8317

at distance 2.225 which is larger than the table limit 2.098 nm.

This is likely either a 1,4 interaction, or a listed interaction inside

a smaller molecule you are decoupling during a free energy calculation.

Since interactions at distances beyond the table cannot be computed,

they are skipped until they are inside the table limit again. You will

only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is

probably something wrong with your system. Only change the table-extension

distance in the mdp file if you are really sure that is the reason.

WARNING: Listed nonbonded interaction between particles 6651 and 6654

at distance 2.126 which is larger than the table limit 2.098 nm.