运行plumed funnel-md报错求助

watermelon_

我使用的plumed.dat文件是

d1: DISTANCE ATOMS=2839,197

lig: COM ATOMS=2833,2834,2835,2836,2837,2838,2839,2840,2841,2842,2843,2844,2845,2846,2847,2848,2849,2850,2851,2852,2853,2854,2855,2856,2857,2858,2859,2860,2861,2862,2863,2864,2865,2866,2867,2868,2869,2870,2871,2872,2873,2874,2875,2876,2877,2878,2879

fps: FUNNEL_PS LIGAND=lig REFERENCE=npt.gro ANCHOR=2455 POINTS=8.043,6.969,3.992,2.689,3.88,0.28

PRINT ARG=fps.lp,fps.ld

FUNNEL ARG=fps.lp,fps.ld ZCC=8.0 ALPHA=0.55 RCYL=0.1 MINS=-0.08 MAXS=8.05 KAPPA=35100 NBINS=500 NBINZ=500 FILE=BIAS LABEL=funnel

# remove BIASFACTOR if you want to perform standard metadynamics
METAD ARG=d1 SIGMA=0.01 HEIGHT=2.0 PACE=500 TEMP=300 BIASFACTOR=20 GRID_MIN=0.0 GRID_MAX=80.0 GRID_BIN=40000 CALC_RCT RCT_USTRIDE=1 LABEL=metad

LOWER_WALLS ARG=fps.lp AT=-0.03 KAPPA=500000 EXP=2 OFFSET=0 LABEL=lwall

UPPER_WALLS ARG=fps.lp AT=8.0 KAPPA=500000 EXP=2 OFFSET=0 LABEL=uwall

PRINT STRIDE=500 ARG=* FILE=COLVAR



然后报错的内容是

Unknown exception:
(exception type: N4PLMD6Plumed14ExceptionErrorE)

(tools/Grid.cpp:168) GridBase::index_t PLMD::GridBase::getIndex(const
std::vector<unsigned int> &) const
Looking for a value outside the grid along the 0 dimension (arg name: fps.lp)

The above exception was the direct cause of the following exception:

(core/PlumedMain.cpp:972) void PLMD::PlumedMain::justCalculate()
An error happened while calculating funnel

watermelon_

有试过把GRID_MAX增加10倍和100倍 但是没有效果

student0618

Metad 的grid max 太大了，当然会跑出funnel 轴的 max (fps.lp)。注意funnel和metad 的grid min/max 都要恰当设定。

开始时小分子应该要在funnel内，用vmd的plugin检查一下。
也要确保Metadynamics不会跑出funnel min/max (可检查fps.lp 是不是到min/max 了), 是的话d1也要加wall。
也有可能是pbc问题, 先试试加WHOLMOLECULES。
或者Anchor atom可能要改。

以上解决方案来自下文：
Funnel metadynamics的nature protocol是他真正的手册，非常详尽，有常见问题解决方法。见 https://doi.org/10.1038/s41596-020-0342-4


一点心得：跑Funnel metadynamics很常跑一半崩溃。常见原因有Looking for a value outside the grid along the 0 dimension (arg name: fps.lp)

• 检查各CV及轨迹后改输入文件，我试过是funnel太大结果ligand跑到蛋白另一边回不去只能跑到funnel外导致崩溃。
• 如果是pbc的问题而WHOLMOLECULE解决不到也可能要加大盒子
• Metad bias的CV 也可能要加wall 免得跑到fps.lp min/max 以外
  

还有metad out of grid

• 这可用恰当的wall解决，较容易处理。
  

watermelon_

student0618 发表于 2024-10-30 12:05
Metad 的grid max 太大了，当然会跑出funnel 轴的 max (fps.lp)。注意funnel和metad 的grid min/max 都要恰 ...

感谢分享！！
我重新生成了plumed文件，添加了WHOLEMOLECULES，并把GRID_MAX减小了很多，配体目前还在漏斗内，但还是运行step0之后就断开了
文件如下
WHOLEMOLECULES ENTITY0=1-2879

d1: DISTANCE ATOMS=2839,197

lig: COM ATOMS=2833,2834,2835,2836,2837,2838,2839,2840,2841,2842,2843,2844,2845,2846,2847,2848,2849,2850,2851,2852,2853,2854,2855,2856,2857,2858,2859,2860,2861,2862,2863,2864,2865,2866,2867,2868,2869,2870,2871,2872,2873,2874,2875,2876,2877,2878,2879

fps: FUNNEL_PS LIGAND=lig REFERENCE=npt.gro ANCHOR=2030 POINTS=8.043,6.969,3.992,2.689,3.88,0.28

PRINT ARG=fps.lp,fps.ld,d1

FUNNEL ARG=fps.lp,fps.ld ZCC=8.0 ALPHA=0.55 RCYL=0.1 MINS=-0.08 MAXS=8.05 KAPPA=35100 NBINS=500 NBINZ=500 FILE=BIAS LABEL=funnel

# remove BIASFACTOR if you want to perform standard metadynamics
METAD ARG=d1 SIGMA=0.01 HEIGHT=2.0 PACE=500 TEMP=300 BIASFACTOR=20 GRID_MIN=0.0 GRID_MAX=0.16 GRID_BIN=80 CALC_RCT RCT_USTRIDE=1 LABEL=metad

LOWER_WALLS ARG=fps.lp AT=-0.03 KAPPA=500000 EXP=2 OFFSET=0 LABEL=lwall

UPPER_WALLS ARG=fps.lp AT=8.0 KAPPA=500000 EXP=2 OFFSET=0 LABEL=uwall

PRINT STRIDE=500 ARG=* FILE=COLVAR
于是换了个报错
Unknown exception:
(exception type: N4PLMD6Plumed14ExceptionErrorE)

(tools/Grid.cpp:168) GridBase::index_t PLMD::GridBase::getIndex(const
std::vector<unsigned int> &) const
Looking for a value outside the grid along the 0 dimension (arg name: d1)

The above exception was the direct cause of the following exception:

(core/PlumedMain.cpp:972) void PLMD::PlumedMain::justCalculate()
An error happened while calculating metad
我尝试添加了
LOWER_WALLS ARG=d1 AT=-0.03 KAPPA=500000 EXP=2 OFFSET=0 LABEL=dlwall

UPPER_WALLS ARG=d1 AT=8.0 KAPPA=500000 EXP=2 OFFSET=0 LABEL=duwall
然而还是Looking for a value outside the grid along the 0 dimension (arg name: d1)
您能再看看哪里要改嘛

student0618

metad bias的cv是d1， grid max是0.16 但d1 的uwall是8？(感觉0.16是否错了？) 哪个才对？uwall要小于grid max才能限制他哦？