计算化学公社

标题: gromacs的能量最小化过程中不收敛 [打印本页]

作者
Author: rugals 时间: 2022-10-22 20:41
标题: gromacs的能量最小化过程中不收敛
模拟100个聚合物链状分子，聚合度15，全是直链。
gro文件由packmol生成，itp由sobtop按照其主页的例5生成。盒子大小基本上能刚好满足塞进所有分子。
EM只跑了一步就停了。提示最大受力过大，且不可能收敛。生成的gro文件中有两个分子链跑到盒子外面去了。
系统用的是sob老师编译的gromacs2018 win64版。
请问是聚合物构象的原因还是盒子太小的原因，或者是别的原因？

界面提示：
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.

Polak-Ribiere Conjugate Gradients converged to machine precision in 0 steps,
but did not reach the requested Fmax < 100.
Potential Energy  =  1.0651435e+10
Maximum force    =  2.9223842e+12 on atom 1639
Norm of force    =  3.3802336e+10

附mdp文件：
; pre-process
define = -DFLEXIBLE

; operation
integrator = cg
nsteps = 10000
dt =0.001

; energy minimization parameters
emtol  = 100.0
emstep = 0.01
nstcgsteep = 1000

; output frequency controlling
nstxout-compressed = 100
nstlog = 100
nstenergy = 100

; neighborlist generation
cutoff-scheme = verlet

; periodic setting
pbc = xyz

; electrostatic and van de waals effects
coulombtype             = PME
rcoulomb                = 1.0
vdwtype                = Cut-off
rvdw                   = 1.0
DispCorr                = EnerPres

; constraints on bonds
constraints             = none

作者
Author: sobereva 时间: 2022-10-22 21:18
先跑单个分子看看情况

作者
Author: rugals 时间: 2022-10-23 14:56

sobereva 发表于 2022-10-22 21:18
先跑单个分子看看情况

单个分子能够收敛，但分子构象上变化不太大基本还是直的。
log文件的最后几行：

Step          Time
         142    142.00000

Energies (kJ/mol)
         Bond       Angle Proper Dih.  Improper Dih.       LJ-14
7.81872e+01 1.64513e+02 3.10271e+02 2.45096e-03 9.85756e+01
   Coulomb-14       LJ (SR)  Disper. corr. Coulomb (SR) Coul. recip.
-6.27383e+01 7.16339e+01 -2.12866e-01 -4.41992e+00 4.39707e+00
   Potential Pres. DC (bar) Pressure (bar)
6.60209e+02 0.00000e+00 -1.97073e-02

Polak-Ribiere Conjugate Gradients converged to Fmax < 100 in 142 steps
Potential Energy  =  6.6020886e+02
Maximum force    =  9.6624550e+01 on atom 128
Norm of force    =  3.6380859e+01

Performed 182 energy evaluations in total.
Finished mdrun on rank 0 Sun Oct 23 14:55:27 2022

作者
Author: sobereva 时间: 2022-10-24 05:05

rugals 发表于 2022-10-23 14:56
单个分子能够收敛，但分子构象上变化不太大基本还是直的。
log文件的最后几行：

直的很正常

初始结构里把分子摆得分散点再试，如果很分散依然不行，也许拓扑文件有问题或者和结构文件对应关系有问题之类

作者
Author: rugals 时间: 2022-10-24 11:01

sobereva 发表于 2022-10-24 05:05
直的很正常

初始结构里把分子摆得分散点再试，如果很分散依然不行，也许拓扑文件有问题或者和结构文件 ...

谢谢老师，加大盒子尺寸后能够收敛

欢迎光临计算化学公社 (http://bbs.keinsci.com/)