adding rgy example notebook

mdagent/tools/base_tools/simulation_tools/create_simulation.py

@@ -140,7 +140,7 @@ class ModifyBaseSimulationScriptTool(BaseTool):
     requirement and returns a modified script. """
 
     args_schema = ModifyScriptInput
-
+    llm: Optional[BaseLanguageModel]
     path_registry: Optional[PathRegistry]
 
     def __init__(self, path_registry: Optional[PathRegistry], llm: BaseLanguageModel):

mdagent/tools/maketools.py

@@ -8,7 +8,6 @@
 from langchain.embeddings.openai import OpenAIEmbeddings
 from langchain.tools import BaseTool, StructuredTool
 from langchain.vectorstores import Chroma
-from langchain_experimental.tools import PythonREPLTool
 from pydantic import BaseModel, Field
 
 from mdagent.subagents import Iterator, SubAgentSettings
@@ -68,7 +67,7 @@ def make_all_tools(
 
     if llm:
         all_tools += agents.load_tools(["llm-math"], llm)
-        all_tools += [PythonREPLTool()]  # or PythonREPLTool(llm=llm)?
+        # all_tools += [PythonREPLTool()]  # or PythonREPLTool(llm=llm)?
         if human:
             all_tools += [agents.load_tools(["human"], llm)[0]]
 

notebooks/log.txt

@@ -0,0 +1,111 @@
+#"Step"	"Potential Energy (kJ/mole)"	"Temperature (K)"
+100	-6947.2247032487	215.14497901895803
+200	-6606.755809423742	245.3241393007874
+300	-6455.50458917632	260.51263456655107
+400	-6417.584625724892	270.5266431819455
+500	-6387.242479160466	284.2023861024972
+600	-6388.191513396453	304.75129960317236
+700	-6527.962233533835	312.77642726121877
+800	-6580.485359734401	308.49461952430136
+900	-6639.961133942442	310.8474107717545
+1000	-6738.569551178414	311.32317014735116
+100	-6763.010282594562	308.34238602524323
+200	-6864.593446104183	297.14596179605235
+300	-6994.262937386531	301.6155468915757
+400	-6935.3252492052625	302.840190711954
+500	-6884.12007129439	308.5139534209478
+600	-6823.701590637071	294.57380936407344
+700	-7098.962557341907	309.49755996420396
+800	-7051.7452111275	322.37169817500165
+900	-6978.0344834561865	314.9502828703213
+1000	-7056.721987246631	303.968134836879
+1100	-7046.6999714784815	306.0755016850859
+1200	-7048.322404235125	305.6905864146254
+1300	-7268.2398016023835	297.76124633020316
+1400	-7142.712178509726	302.5973284852797
+1500	-7074.607665958954	304.7594080228363
+1600	-7054.775157890861	306.2956050961427
+1700	-7302.195431149743	314.77506377149166
+1800	-7077.27914964579	295.2082987290798
+1900	-7245.591044039093	296.544622044704
+2000	-7212.115861307699	319.23831684768015
+2100	-7106.951554771362	309.73032179563535
+2200	-7228.607015852927	319.90152415467907
+2300	-7143.259374447855	313.9650423015229
+2400	-7090.197770676733	300.68065743983993
+2500	-7143.99685820832	295.2536934381932
+2600	-7098.832476661368	300.0048777407126
+2700	-7268.647665059764	298.826501443611
+2800	-7336.104454383806	294.3819777240061
+2900	-7336.591976045821	307.74503069963805
+3000	-7057.30711976404	293.5014579323123
+3100	-7213.7130508119935	309.9046472913062
+3200	-7133.936614433825	300.28469131884924
+3300	-7313.628574393655	308.0010973022024
+3400	-7288.408543498386	294.99061245573716
+3500	-7304.36953833251	310.5039921062637
+3600	-7345.088882165166	305.5070448590426
+3700	-7403.013975376743	302.30178732665496
+3800	-7512.509225099482	298.0299395624267
+3900	-7525.509296441533	297.133701097967
+4000	-7442.256195117707	287.8468724980225
+4100	-7484.523602742913	290.17220749793483
+4200	-7427.595767154028	297.6072402367254
+4300	-7442.285244593137	297.949922225918
+4400	-7646.080315335545	303.5556593818187
+4500	-7509.217638774311	295.1847760307521
+4600	-7588.969875899482	304.89273307268104
+4700	-7593.136272293861	314.3357662335734
+4800	-7408.754119323856	299.4101954654273
+4900	-7518.519963034358	308.4406384054823
+5000	-7335.847583024362	297.9900941455528
+5100	-7343.644451228044	299.6446536189008
+5200	-7463.402653954167	301.29974167930163
+5300	-7315.594154268405	302.884395290947
+5400	-7479.829920624285	312.9141326975404
+5500	-7421.622820649305	294.94611914342613
+5600	-7331.638008310608	312.5316794090319
+5700	-7503.422662571294	299.9222304814086
+5800	-7407.9934910453585	302.7387451361232
+5900	-7434.610959625382	307.05171580365544
+6000	-7635.108450163959	311.4037619992867
+6100	-7560.147899779708	313.1264421995106
+6200	-7395.727234281008	299.92308568439176
+6300	-7456.229042733998	313.9068496278615
+6400	-7499.692522152247	312.73399827946355
+6500	-7396.250204244039	309.6537941646525
+6600	-7479.857365188253	303.5751917374244
+6700	-7509.906941008841	305.6478411694014
+6800	-7532.351882028655	300.5579748382905
+6900	-7494.858360312032	308.49406582763913
+7000	-7668.005793912738	313.47348679905707
+7100	-7513.358410033883	305.38889505182146
+7200	-7547.72842265137	298.75230254494153
+7300	-7550.496783298053	293.1341975953963
+7400	-7471.110704957506	296.01806695990757
+7500	-7306.0955198705815	296.76211917341044
+7600	-7456.7088101530335	314.00429120219945
+7700	-7451.0343175692	307.96915807036993
+7800	-7503.60657165548	312.0347806234592
+7900	-7470.824045148967	303.6361298742164
+8000	-7555.068396550282	302.9276076921207
+8100	-7610.5951014659	295.6803480784775
+8200	-7674.049061292562	299.0771096466942
+8300	-7460.8241791704095	296.7879063419885
+8400	-7526.390876454641	293.55941336014234
+8500	-7512.653204235832	302.3546395658116
+8600	-7499.334945839408	293.8962556388488
+8700	-7624.077188836976	294.0369602357294
+8800	-7589.509712028355	280.0209964060526
+8900	-7564.679421422048	293.07969824131726
+9000	-7527.198853002337	292.2184929509117
+9100	-7600.598122097535	305.5898863653994
+9200	-7600.935021774027	308.0925393412393
+9300	-7662.005988771483	301.1850411356524
+9400	-7593.028662043358	294.9501713882646
+9500	-7476.491493208251	296.21756803567155
+9600	-7695.3925753276	310.4407903303529
+9700	-7641.082924787625	307.1439616533547
+9800	-7572.797165494741	291.74075129818596
+9900	-7489.361064130782	291.1752541137238
+10000	-7548.086623141088	288.4769029339633

notebooks/radius_of_gyration.txt

@@ -0,0 +1,19 @@
+[1.50767929 1.50682119 1.50068744 1.4941606  1.48222915 1.47337426
+ 1.46404147 1.46070665 1.45946214 1.46320232 1.46158771 1.4667646
+ 1.46855866 1.46025191 1.45444605 1.4486515  1.44307955 1.44337105
+ 1.44779935 1.45570087 1.46238626 1.45914084 1.45751507 1.46000107
+ 1.45722055 1.45690918 1.46324583 1.46327771 1.46135877 1.46398437
+ 1.45960216 1.45687341 1.44958755 1.44901427 1.44655509 1.44219043
+ 1.44038892 1.43712164 1.43932839 1.43726949 1.42746745 1.42639579
+ 1.42101927 1.42325591 1.43352625 1.4339341  1.42705837 1.42664298
+ 1.42637167 1.4223091  1.42854714 1.43482307 1.44154946 1.44525946
+ 1.44147111 1.4423343  1.44247447 1.44444753 1.44005083 1.43315945
+ 1.42947646 1.42474755 1.42775308 1.42855768 1.42934235 1.43771966
+ 1.44039219 1.43247868 1.42939829 1.43404689 1.4340275  1.43823166
+ 1.44255801 1.44040663 1.44563689 1.44141945 1.43733975 1.43698322
+ 1.43267958 1.43943851 1.45250143 1.46383664 1.45774152 1.44849624
+ 1.44803498 1.44447058 1.44255154 1.44416815 1.44473221 1.44208753
+ 1.44139582 1.44445096 1.44170214 1.44497769 1.44309719 1.44453544
+ 1.44245933 1.43739164 1.43132974 1.43106005 1.43755989 1.43798897
+ 1.43229375 1.43462052 1.43297028 1.43080176 1.43166855 1.42949051
+ 1.43134256 1.42874934]

notebooks/reproduce_simulation.py

@@ -0,0 +1,80 @@
+# This script was generated by MDagent-Setup.
+
+from openmm import *
+from openmm.app import *
+from openmm.unit import *
+
+# Input Files
+pdb = PDBFile("cleaned_fibronectin.pdb")
+forcefield = ForceField("amber14-all.xml", "amber14/tip3p.xml")
+
+# System Configuration
+nonbondedMethod = NoCutoff
+constraints = AllBonds
+rigidWater = True
+constraintTolerance = 1e-05
+
+# Integration Options
+dt = 0.004 * picosecond
+temperature = 300 * kelvin
+friction = 1.0 / picosecond
+
+# Simulation Options
+steps = 10000
+equilibrationSteps = 1000
+platform = Platform.getPlatformByName("CPU")
+dcdReporter = DCDReporter("trajectory.dcd", 10000)
+dataReporter = StateDataReporter(
+    "log.txt",
+    100,
+    totalSteps=steps,
+    step=True,
+    speed=True,
+    progress=True,
+    elapsedTime=True,
+    remainingTime=True,
+    potentialEnergy=True,
+    temperature=True,
+    volume=True,
+    density=True,
+    separator="	",
+)
+checkpointReporter = CheckpointReporter("checkpoint.chk", 10000)
+
+# Minimize and Equilibrate
+# ... code for minimization and equilibration ...
+
+# Simulate
+
+print("Building system...")
+topology = pdb.topology
+positions = pdb.positions
+
+system = forcefield.createSystem(
+    topology,
+    nonbondedMethod=nonbondedMethod,
+    constraints=constraints,
+    rigidWater=rigidWater,
+)
+
+integrator = LangevinMiddleIntegrator(temperature, friction, dt)
+integrator.setConstraintTolerance(constraintTolerance)
+simulation = Simulation(topology, system, integrator, platform)
+simulation.context.setPositions(positions)
+
+# Minimize and Equilibrate
+
+print("Performing energy minimization...")
+simulation.minimizeEnergy()
+print("Equilibrating...")
+simulation.context.setVelocitiesToTemperature(temperature)
+simulation.step(equilibrationSteps)
+
+# Simulate
+
+print("Simulating...")
+simulation.reporters.append(dcdReporter)
+simulation.reporters.append(dataReporter)
+simulation.reporters.append(checkpointReporter)
+simulation.currentStep = 0
+simulation.step(steps)