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标题: 求助-PLUMED+GROMACS跑 funnel metadynamics 报错 [打印本页]

作者
Author: hpz1994 时间: 2025-4-24 16:26
标题: 求助-PLUMED+GROMACS跑 funnel metadynamics 报错
我打算用funnel metadynamics计算一个小分子配体和受体之间的结合能，然后照着PLUMED的官方教程去做，然后一开始模拟就报错，但是普通MD可以正常跑完，表明我的结构和拓扑应该没问题。
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Program: gmx mdrun, version 2024.3-plumed_2.9.3

Unknown exception:
(exception type: N4PLMD6Plumed14ExceptionErrorE)

(tools/Grid.cpp:168) PLMD::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

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/curre ... un-time-errors.html
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这是我利用FMAP输出的PLUMED输入文件上修改的：
MOLINFO STRUCTURE=ref2.pdb
WHOLEMOLECULES ENTITY0=1-4811
WHOLEMOLECULES ENTITY0=4812-4853
c1: CENTER ATOMS=4812-4853
c2: CENTER ATOMS={@mda:{name CA and resid 24:29:254:259:262}}
lig: COM ATOMS=4812,4813,4814,4815,4816,4817,4818,4819,4820,4821,4822,4823,4824,4825,4826,4827,4828,4829,4830,4831,4832,4833,4834,4835,4836,4837,4838,4839,4840,4841,4842,4843,4844,4845,4846,4847,4848,4849,4850,4851,4852,4853
d1: DISTANCE ATOMS=c1,c2

fps: FUNNEL_PS LIGAND=lig REFERENCE=ref2.pdb ANCHOR=4171 POINTS=3.048,1.843,3.653,3.126,1.469,4.468

FUNNEL ARG=fps.lp,fps.ld ZCC=1.5 ALPHA=0.6 RCYL=0.2 MINS=0.00 MAXS=4.00 KAPPA=35000 NBINS=500 NBINZ=500 FILE=BIAS LABEL=funnel

#METAD ARG=d1 SIGMA=0.015 HEIGHT=0.7 PACE=500 TEMP=298.15 BIASFACTOR=15 GRID_MIN=0.00 GRID_MAX=6.00 GRID_BIN=500 CALC_RCT RCT_USTRIDE=1 LABEL=metad

LOWER_WALLS ARG=fps.lp AT=0.40 KAPPA=35000 EXP=2 OFFSET=0 LABEL=lwall

UPPER_WALLS ARG=fps.lp AT=3.80 KAPPA=35000 EXP=2 OFFSET=0 LABEL=uwall

UPPER_WALLS ARG=d1 AT=4.10 KAPPA=35000 EXP=2 OFFSET=0 LABEL=distwall

UPPER_WALLS ARG=fps.ld AT=0.09 KAPPA=35000 EXP=2 LABEL=ld_wall

PRINT STRIDE=250 ARG=d1,fps.* FILE=COLVAR
我也把结构拓扑文件上传了，望大佬帮助。

作者
Author: student0618 时间: 2025-4-24 17:27
Funnel metadynamics的nature protocol有常见问题的解决方案的，参考我在这帖的连结和截图 http://bbs.keinsci.com/forum.php ... 0&fromuid=64740

作者
Author: hpz1994 时间: 2025-4-24 20:15

student0618 发表于 2025-4-24 17:27
Funnel metadynamics的nature protocol有常见问题的解决方案的，参考我在这帖的连结和截图 http://bbs.kein ...

谢谢

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