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标题: martini跑蛋白和极化水体系的NVT时遇到问题 [打印本页]

作者
Author: yuhai 时间: 2021-7-1 15:54
标题: martini跑蛋白和极化水体系的NVT时遇到问题
sob老师，您好我在martini跑蛋白和极化水体系中，跑nvt遇到这样的问题，请问这么解决
WARNING 1 [file CG.top, line 18]

The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times  the time step of 2.0e-02 ps.  Maybe you forgot to change the constraints mdp option.

我的mdp文件，其他都是正常的设置。
; Bond parameters
constraints          = none    ; No constraints except for those defined explicitly in the topology
constraint_algorithm = Lincs    ; LINear Constraint Solver
continuation          = no       ;
lincs_order          = 4       ; also related to accuracy
lincs_iter          = 1       ; accuracy of LINCS
lincs_warnangle       = 90    ; maximum angle that a bond can rotate before LINCS will complain

这虽然是个警告，-maxwarning 1可以是模拟进行，但是后面就会报原子超出约束90  我想了一些方法解决这个问题，但是还是报错

[td]Step 435516, time 2177.58 (ps)  LINCS WARNING relative constraint deviation after LINCS:
rms 0.110531, max 11.324476 (between atoms 89 and 90)
bonds that rotated more than 90 degrees: atom 1 atom 2  angle  previous, current, constraint length
Wrote pdb files with previous and current coordinates[/td]
恳请sob老师指教！

作者
Author: nianbin 时间: 2021-7-1 20:13
constraints=hbonds

作者
Author: yuhai 时间: 2021-7-1 20:27
粗粒化中极化水中有氢键吗

作者
Author: sobereva 时间: 2021-7-2 01:58
constraints = all-bonds或者减小步长再试

如置顶的新社员必读贴、论坛首页的公告栏、版头的红色大字非常明确所示，求助帖必须在帖子标题明确体现出此帖内容是求助或提问，并清楚反映出帖子具体内容，避免有任何歧义，仔细看http://bbs.keinsci.com/thread-9348-1-1.html。我已把你的严重不恰当标题“模拟蛋白在极化水”改了，以后务必注意

作者
Author: 王子璇 时间: 2022-9-19 09:44

sobereva 发表于 2021-7-2 01:58
constraints = all-bonds或者减小步长再试

如置顶的新社员必读贴、论坛首页的公告栏、版头的 ...

老师修改过后，平衡相模拟：
gmx grompp -f eq.mdp -c em.gro -p topol.top -o eq.tpr -r em.gro
运行成功，但是mdrun的时候出现了以下问题
gmx mdrun -v -deffnm eq

Using 1 MPI thread
Using 4 OpenMP threads

WARNING: Using the slow plain C kernels. This should
not happen during routine usage on supported platforms.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 4.589765, max 152.877777 (between atoms 32729 and 32730)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
Wrote pdb files with previous and current coordinates

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2169.020020, max 92229.296875 (between atoms 32729 and 32730)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   1    4 85.7 0.1476  14.3722    0.1493
   1    27  117.6 0.7739  87.7616    0.1826
   1    33  142.4 0.1979  34.8137    0.1848
   1    39 99.7 0.2540 3.7037    0.2763
   2    5  153.7 0.3052 118.3330    0.1465
......
  32822  32825 75.5 0.1012 2.9946    0.0960
  32823  32825 57.8 0.1517 108.2485    0.1566
  32822  32824 84.3 0.1004 4.0798    0.0961
  32823  32824 76.1 0.1591  97.6529    0.1567

-------------------------------------------------------
Program:    gmx mdrun, version 2018.8
Source file: src/gromacs/mdlib/constr.cpp (line 169)

Fatal error:
Too many LINCS warnings (1379)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

请问各位老师，怎么样去修改mdp文件呢
define = -DPOSRES
integrator = md
dt       = 0.002  ; ps
nsteps    = 100000 ; 200ps
comm-grps  = system
energygrps =
energygrp-excl =
;
nstxout = 0
nstvout = 0
nstfout = 0
nstlog  = 500
nstenergy = 500
nstxout-compressed = 1000
compressed-x-grps  = system
;
annealing = single
annealing_npoints = 2
annealing_time = 0 100 ;ps
annealing_temp = 0 298.15
;
periodic-molecules = yes
pbc          = xyz
cutoff-scheme = verlet
nstlist       = 10
rlist       = 1.2
coulombtype = PME
rcoulomb    = 1.2
vdwtype    = cut-off
rvdw       = 1.2
DispCorr    = EnerPres
;
Tcoupl  = V-rescale
tau_t = 0.2
tc_grps = system
ref_t = 298.15
;
Pcoupl    = Berendsen
pcoupltype = isotropic
tau_p = 0.5
ref_p = 1.0
compressibility = 4.5e-5
refcoord_scaling = all
;
gen_vel  = no
gen_temp = 298.15
gen_seed = -1
;
freezegrps  =
freezedim =
constraints = all-bonds

作者
Author: k64_cc 时间: 2022-9-19 10:10
虽然我知道NVT里dispersion correction无所谓，不过DispCorr最好关一下。

作者
Author: qingqingdong 时间: 2023-1-3 16:54

王子璇发表于 2022-9-19 09:44
老师修改过后，平衡相模拟：
gmx grompp -f eq.mdp -c em.gro -p topol.top -o eq.tpr -r em.gro
运行 ...

请问你的问题解决了吗，我在做蛋白质的MD中，进行限制性动力学时也出现了这个问题

作者
Author: echo112 时间: 2023-2-21 15:51
请问问题解决了吗我跑gromacs的油水体系的时候也出现了同样的问题可以解答一下吗

作者
Author: jiangyan 时间: 2024-6-17 09:24

echo112 发表于 2023-2-21 15:51
请问问题解决了吗我跑gromacs的油水体系的时候也出现了同样的问题可以解答一下吗

我也是油水体系碰到了类似的问题，可以说一下是怎么解决的吗

作者
Author: HNUST 时间: 2025-9-26 09:17

jiangyan 发表于 2024-6-17 09:24
我也是油水体系碰到了类似的问题，可以说一下是怎么解决的吗

大佬可以说一下是怎么解决的吗

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