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标题: Gromac跑膜的溶胀，运行NVT正常，但运行NPT初始就报错 [打印本页]

作者
Author: 小心怪 时间: 2022-4-22 11:18
标题: Gromac跑膜的溶胀，运行NVT正常，但运行NPT初始就报错
在跑膜的溶胀，盒子比较细长在2.6×2.7×13，可以正常跑有退火的NVT，但一跑NPT还没跑就报错，是因为NVT平衡没跑平衡吗？

NPT控制文件如下：
; RUN CONTROL PARAMETERS
integrator             = md
; Start time and timestep in ps
tinit                   = 0
dt                      = 0.001
nsteps                = 1000000
; For exact run continuation or redoing part of a run
init-step             = 0
; mode for center of mass motion removal
;comm-mode             = Linear

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                = 10000
nstvout                = 10000
; Output frequency for energies to log file and energy file
nstlog                = 10000
nstenergy             = 10000

; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps       = system
; Selection of energy groups
energygrps             = PDMS SOL

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                = 10
; Periodic boundary conditions: xyz, no, xy
pbc                   = xyz
; nblist cut-off
rlist                   = 1.2  ;nm !

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype             = PME
rcoulomb                = 1.2 ;nm  !
; Method for doing Van der Waals
vdw-type                = Cut-off
; cut-off lengths
rvdw                   = 1.2 ;nm  !
; Spacing for the PME/PPPM FFT grid
fourierspacing          = 0.16
; EWALD/PME/PPPM parameters
pme_order             = 4
;ewald_rtol             = 1e-05

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                = V-rescale;
; Groups to couple separately
tc-grps                = System ;
; Time constant (ps) and reference temperature (K)
tau_t                   = 0.1 ;
ref_t                   = 300 ;

; pressure coupling
pcoupl                = berendsen
pcoupltype             = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                   = 2.0 2.0
compressibility       = 4.5e-5 4.5e-5
ref_p                   = 1.0 1.0

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                = no
; Dispersion correction
DispCorr                = EnerPres  ; account for cut-off vdW scheme

报错：
step 0: Water molecule starting at atom 7111 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 0: Water molecule starting at atom 12403 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 0: Water molecule starting at atom 9796 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 0: Water molecule starting at atom 11560 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 0: Water molecule starting at atom 11668 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 0: Water molecule starting at atom 9565 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
~~~~~~~
A list of missing interactions:
            Bond of 3982 missing    3
            Angle of 7488 missing    10
      Proper Dih. of 9370 missing    27
      exclusions of  29604 missing    42

Molecule type 'PDMS'
the first 10 missing interactions, except for exclusions:
      Proper Dih. atoms  654  645  646  649 global 654 645 646 649
            Angle atoms  825 3289 3280    global 825  3289  3280
            Angle atoms  825  834 2218    global 825 834  2218
      Proper Dih. atoms  826  825  834 2218 global 826 825 834  2218
      Proper Dih. atoms  826  825 3289 3280 global 826 825  3289  3280
      Proper Dih. atoms  830  825  834 2218 global 830 825 834  2218
      Proper Dih. atoms  830  825 3289 3280 global 830 825  3289  3280
      Proper Dih. atoms  834  825 3289 3280 global 834 825  3289  3280
      Proper Dih. atoms 1411 1422 1427 1428 global  1411  1422  1427  1428
      Proper Dih. atoms 1411 1422 1427 1429 global  1411  1422  1427  1429

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: /home/pengfj/files/gromacs-4.5.5/src/mdlib/domdec_top.c, line: 356

Fatal error:
82 of the 53300 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

作者
Author: 牧生 时间: 2022-4-22 11:47
http://sobereva.com/soft/Sobtop/

看FAQ 8，几乎包罗万象。

作者
Author: 小心怪 时间: 2022-4-22 14:40

牧生发表于 2022-4-22 11:47
http://sobereva.com/soft/Sobtop/

看FAQ 8，几乎包罗万象。

但NVT可以跑，但NPT跑不了应该不是结构和力场的问题吧，其余都就不清楚了

作者
Author: sobereva 时间: 2022-4-22 21:16

小心怪发表于 2022-4-22 14:40
但NVT可以跑，但NPT跑不了应该不是结构和力场的问题吧，其余都就不清楚了

体系用genconf平移复制成原先的2*2*1大小再试

作者
Author: EdwardLimit 时间: 2022-4-23 11:27
tau_p                   = 1.0 1.0
compressibility       = 0 4.5e-5
ref_p                   = 0.0 1.0
改成这个试试，另外PDMS水溶胀我做过相关工作，可以加好友交流

作者
Author: xiaoruoqiu 时间: 2022-8-25 22:18

EdwardLimit 发表于 2022-4-23 11:27
tau_p                   = 1.0 1.0
compressibility       = 0 4.5e-5
ref_p                   =  ...

请问可否提供PDMS力场文件和相关咨询，有偿

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