Insight II 400PIncluding Polymer 10.0

Release NotesApril, 1998

Welcome to Insight II version 400P, the latest release of the Accelrys's Polymer Modelingtools including Polymer 10.0. This release builds upon the prior version 4.0.0 release andintroduces several new capabilities, improvements and updates. This document describes the newfeatures, enhancements, and known and fixed problems in Polymer 10.0 for each of the following:

Installation Notes

Amorphous_CellDiscover

FlexiblendNetworks

Hypertext DocumentationCOMPASS forcefield

MD_ReactTransition State Theory Diffusion

RIS

Amorphous_Cell

Amorphous_Cell Protocols

Two new Amorphous_Cell protocols (accessed via the AC_Refine/Protocol_Run command)have been developed as follows:

Polarization/Dielectric Behavior

Permits you to investigate the effects of external electric fields on bulk periodic systems. Asingle invocation of the protocol can perform a series of molecular dynamics simulations atdifferent field strengths. The polarization of the material is computed at intervals duringeach stage, with results saved in standard .tbl files.

Thermal Diffusion

Uses Discover to set up an initial step temperature gradient in a bulk periodic system.

Broadening of the profile during subsequent molecular dynamics simulation is monitored toestimate thermal diffusivity of the material.

Amorphous_Cell Analysis

It is now possible to investigate the mutual orientational correlation of pairs of dissimilar bondswhen using the Orientational_Correlation Property available through the AC_Analyze/Setupcommand. This can be used, for example, to investigate preferred orientation involved in specificinteractions (such as -C=O and -O-H bonds in carboxylic acids, or bonds involved in specificinteractions at surfaces.)

The following bugs have been corrected:

A problem which caused scrambling of some of the tessellation properties written to .tblfiles when using the Voronoi property (for example, p(V) vs. V).

1.

A memory-corruption error which caused the free volume background job to crash whenperforming calculations using the Voorintholt method.

2.

DiscoverSeveral new Discover features are now available via the Insight II graphical user interface:

The periodic cell multipole method (PCMM) for evaluating nonbonds can now be applied toperiodic systems (such as those constructed using Amorphous_Cell). Using the PCMMapproach avoids having to define neutral charge groups to ensure accurate calculations ofelectrostatic nonbond energies and forces. The computational performance (that is, speed) ofPCMM lies between that of the group-based cutoff approach and the Ewald summationmethod (but much closer to the former). Detailed discussion of nonbond methods for use insimulations of periodic systems is provided in the hypertext documentation sources (bothAmorphous_Cell and Discover) described in the Hypertext Documentation and Helpsection of these notes. This feature is found in the Specify/Nonbonds command of theDiscover_3 module.

Application of automatic tail corrections to the energy and stress tensor/pressure may nowbe specified when cutoffs are applied to nonbond interactions in simulations initiated via theuser interface. This feature is accessed via the Tail Correction option in theSpecify/Nonbonds command of the Discover_3 module.

A new Fields command has been added to the Specify pulldown of the Discover_3 module.Using this command you may control the application of Electric fields of any strength ordirection during minimization or dynamics. You may also set up application of Wallpotentials which have the effect of confining the simulated material between opposite facesof a periodic cell. Specifying one, two, or three parallel faces allows preparation of"2-dimensional" slabs, "1-dimensional" rods, and cubes (parallelepipeds) of confinedmaterial respectively.

The default pressure control method applied to NPT calculations has been changed to usethe Berendsen algorithm. Usage of this barostat has been extensively validated duringcalculations performed with the new COMPASS forcefield (though the forcefield

parameterization process itself used only NVT simulations).

Finally, a bug which prevented setting up distance or angle restraints within the userinterface has been corrected.

FlexiblendA bug which caused standard deviations of mixing energies calculated by the Flexib_Analyzecommand to be set to zero has been corrected.

Networks Monte CarloThe Networks Monte Carlo simulation program has been extensively revised. The new version ofthis module now supports reactions between all species in the system. For example, crosslinkersmay react with themselves, and they are allowed to be polymeric. Consequently, direct polymer-polymer reactions are allowed as well.

The use of branched molecules, whether they are combs or stars, is now allowed. Polymers builtwith the branched copolymer options under N_Copolymer are acceptable inputs. At the presenttime, only the Gaussian approximation is allowed for the description of the arm end-junction pointdistribution. Linear molecules continue to offer the option of using an *.riscnf file for descriptionof their configurations.

The algorithm has been improved to better handle the statistics of loop formation in those caseswhere both of the molecules being bonded together contribute substantially to the contour lengthof the growing molecules. This new functionality has been applied to the "linear" urethanepolymerization [see Polym. Int., 44, 311-330 (1997)], where it gives improved agreement withexperimental cyclization data.

The algorithm still uses the capture sphere device, but now you have the option of choosing theincrements (fine, medium, and coarse) between successive values of the capture radius. Thisimproves the speed of the calculation for exploratory work, and conversely improves resolutionfor the most accurate simulations.

Finally, Networks Monte Carlo now offers you the opportunity to output the junction coordinatesand network topology of configurations generated by the module. The Net_MC_Run parameterpanel now contains an option to output structures either at the end of the reaction, or at intervalsspecified in increments of the capture radius. Enabling either of these two options will producepairs of standard .car and .mdf files. The structures in these files may then be visualized using anygraphical modeling system capable of accepting the .car/.mdf format.

Hypertext Documentation and HelpHypertext documentation and help is now available and easily accessible using the DOC buttonlocated on the button bar alongside the Insight II screen. The index page displayed when the DOCbutton is pressed gives access to documentation materials for Discover, Turbomole, and variousPolymer modules, programs and macros. Additional links lead to Discover training for PolymerUsers, and to a convenient index of Insight II commands. Access to further documentation

(including the entire Polymer User Guide) and miscellaneous information at the MSI web site isalso provided for the benefit of users with direct access to the internet. This access may also beobtained using the WWW_Access command in the Help pulldown if you prefer.

Note that this command starts a Netscape web browser (which may take a few seconds dependingon the speed and load of your machine). If another Netscape is already running, you will see awarning that the new browser will not be able to use the disk cache and global history. Thiswarning may safely be ignored.

Note also that if you keep a web browser active continuously, you may prefer simply to bookmarkthe page opened by the DOC button. The button does not then need to be used subsequently.

New COMPASS ForcefieldInsight II version 4.0.0P supports the new COMPASS materials forcefield, and is shipped withversion 1.1. COMPASS (Condensed-phase Optimized Molecular Potentials for AtomisticSimulation Studies) is the product of the extensive 1994-1997 reparameterization of the nonbondparameters (and coupled internals) of the earlier PCFF forcefield, and is the first extensively-parameterized, condensed phase optimized force of its type. Specifically, the parameterizationprocess aims to make possible quantitative prediction of bulk material cohesive properties andPVT behavior. Research conducted to date indicates that COMPASS is able to make quantitativecohesive property/solubility parameter predictions over extended (200-300 degree) temperatureranges, with the ability to predict PVT behavior over similar temperature ranges and pressureranges from at least 0 to 200 MPa. Structures of crystalline materials, while emphasized lessstrongly in the parameterization process than liquid properties, are also generally well reproduced.

The following sections summarize the parameters provided with versions 1.0 and 1.1 ofCOMPASS. For details of planned future releases, refer to the COMPASS pages at the MSI website.

COMPASS Version 1.0

The parameters for the following 28 classes of organic and inorganic molecules are fully validatedand considered final.

AlkanesAlkenesBenzenesAcetylenesAlcoholsEthersSaccharidesAldehydesKetonesAcidsEstersAnhydridesAmines

AmidesCarbonatesCarbamatesFluoro-alkanes (excl. perfluorinated)Chloro-alkanesIsocyanatesNitro derivativesNitrilesSilanesSiloxanesPhosphazenesOrganic sulfur compoundsAmine oxidesSmall (noble and gas) moleculesZeolites

The properties evaluated were:

Molecular structuresConformational propertiesVibrational frequenciesLiquid P-V-T behaviorLiquid cohesive energiesCrystal cell structuresCrystal lattice energies

For functional groups (including organic ions and anions) that consist of the elements H, C, N, O,F, Si, P, S, Cl, Br but are not included in the validation list, COMPASS 1.0 may be useful based onthe assumption of transferability. In addition, this forcefield has a set of approximate parametersfor the following metals:

Ag (Ag), Al (Al), Au (Au), Cr (Cr), Cu (Cu), Fe (Fe), K (K), Li (Li), Mo (Mo), Na(Na), Ni (Ni), Pb (Pb), Pd (Pd), Pt (Pt), Sn (Sn), W (W).

and metal ions:

Ca2+ (ca+), Cs+ (cs+), Cu2+ (cu+2), Fe2+ (fe+2), K+ (k+), Li+ (li+), Mg2+ (mg+2),Na+ (na+), Rb+ (rb+), Zn2+ (zn+2)

COMPASS Version 1.1

Version 1.1 increases the overall coverage of the forcefield. Parameters have been added in twoareas as follows:

Halogenated aromatics.1.Previously-missing parameters for silicon/silica and nitro compounds.2.

Note that these new parameters will not change the results of any calculations performed using theearlier version.

References & Notes

For further details of the parameterization procedures and calculated properties, see:

Sun, H.; Rigby, D. "Polysiloxanes: ab initio forcefield and structural, conformational andthermophysical properties" in Spectrochimica Acta, A53 1301-1323 (1997)

1.

Rigby, D.; Sun, H.; Eichinger, B.E."Computer Simulations of Poly(ethylene oxide): ForceField, PVT Diagrams and Cyclization Behavior". Polymer International, 44, 311-330(1997).

2.

Examples of calculated properties are also included in some of the new Pilot tutorials suppliedwith release 4.0.0P.

The forcefield editor, accessed via the Forcefield/Edit_FF command (or via the FF button), fullysupports COMPASS. You may view and change the values of COMPASS parameters if desired(though making changes is not generally recommended unless the interdependence of parametershas been fully investigated and understood). The software automatically handles decryption of theforcefield file, and will take care of re-encryption should you wish to save a modified version.

Note that the old Discover (v2.9.8) and Crystal Cell modules do not support the COMPASSforcefield.

MD ReactThe MD_React simulation program for studying thermal degradation of polymers and smallmolecules has been extended by Dr. Marc Nyden to handle periodic systems. The macro is alsonow loaded into the AC_Refine pulldown of the Amorphous_Cell module (which providesAmorphous_Cell access to Discover simulations).

If you wish to use MD_React, you must first load the macro by selecting MD_React from the listof macros displayed when the Session/load_macros panel is opened. The macro is then set upwhen you execute load_macros.

Extensive hypertext documentation describing the theory, implementation and use of MD_Reactcan be accessed via a Netscape web browser. See the Hypertext Documentation and Help sectionof these notes for details.

Note that MD_React still currently requires that you use the cvff forcefield.

Transition State Theory DiffusionThe transition state theory approach for studying diffusivity and solubility of small gas moleculesin rigid polymeric matrices is accessible from Insight II version 4.0.0P as two macros, gsnet andgsdif.

If you wish to use gsnet and gsdif, you must first load the macros by selecting TST_Diffusionfrom the list of macros displayed when the Session/load_macros panel is opened. The macro

commands gsnet and gsdif are added to the Custom pulldown when you execute load_macros.

Extensive hypertext documentation describing the implementation, interactive, and standalone useof gsnet and gsdif can be accessed via a Netscape web browser. See the Hypertext Documentationand Help section of these notes for details.

Note that gsnet and gsdif may be used with the COMPASS forcefield.

RIS Metropolis Monte Carlo (RMMC)A memory leak which caused the Insight II version 4.0.0 of RMMC (ris_metrop_mc program) tocrash during long runs has been fixed.

README File Notes on InstallationThe Insight II 400P (I400P) release represents updated versions of Polymer Modules andDiscover. To facilitate swift installation, this update is distributed as an overlay onto your existingInsightII 400 release. In order to properly install I400P, you must NOT remove your existingInsight II 400 installation. If you do not currently have InsightII 400 installed, you must do thisfirst.

To install I400P:

Login as root and source your InsightII 400 cshrc file. You can make sure the file has beensourced by issuing the command:

echo $BIOSYM

It should point to your installation directory.Load the CD in the cdrom. <cd to the /CDROM dir and run:

./I400P_install_patch

You will be asked if you want to save the original files. If you answer 'y' all replacedfiles/dirs will be moved and appended with '.orig'. When the installation is complete, a list ofmoved files (I400_original_files) will be placed in the root I400P installation directory.

NOTE: To revert back to the original I400 installation, manually replace all files anddirectories in the I400_original_files list, and then run the $BIOSYM/install script andselect "Configure/Reconfigure Software".

After the installation finishes, type 'reset_env' before starting InsightII.

Copyright © 1998 Accelrys Inc. All Rights Reserved.Last revised April 3, 1998.