现在发现charmm36力场中，不支持CG321和CG323的键连，不知道是不bug，总是提示No default bond types ...
[ nonbond_params ]; i j func c6 c12 S S 1 0.26171E-02 0.26331E-05...
in this case through a bond between MM atom 1411 (Cα) and QM atom 1413 (Cβ), as well as how to treat the link. We are using the IMOMM method for the link. The arginine sidechain has now been moved to the QM region. This means we need to adjust the QM charge to -...
如果前面x2top时加了-noparam,还需要设定键结参数。分两种情况: 1 直接在.top里面每一个键结项后面加入相应力场参数,类似于x2top自动在.top里添加力场参数的方式,用ultraedit等软件的列模式批量加入效率最高。 2 不在.top里面加,而是在ff???bon.itp里面的[bondtypes] [angletypes] [dihedraltypes]里面加入...
首先加入VDW和1-4VDW参数,分别在ffgmx2nb.itp里的[atomtypes]和[nonbond_params]里面添加。 如果前面x2top时加了-noparam,还需要设定键结参数。分两种情况: 1 直接在.top里面每一个键结项后面加入相应力场参数,类似于x2top自动在.top里添加力场参数的方式,用ultraedit等软件的列模式批量加入效率最高。 2 不...
GROMACS can run in parallel on multiple cores of a single workstation using its built-in thread-MPI. No user action is required in order to enable this. If you wish to run in parallel on multiple machines across a network, you will need to have an MPI library installed that supports the...
gpp_bond_atomtype.cpp insert_molecules.cpp readir.cpp solvate.cpp topdirs.cpp ) # Currently these can be slow to run in Jenkins, so they are in # several test binaries. set(exename pdb2gmx1-test) gmx_add_gtest_executable(${exename} pdb2gmx.cpp ) CPP_SOURCE_FILES pdb2gmx.cpp ) ...
group1 and group2 –name the groups which will be used for pairwise forces calculations; if not present, they default to “Protein”. The 2 groups are equivalent, there is no difference in how they are treated internally. The groups names should exist in the index file specified with the...
(inthiscase,thehelixaxis) alongthez-axisbydefault,butthisoptionhaschangedasofGROMACS-4.0.4,whichorientsthelongaxisalongthex- axis.Ifyouwanttoskiptheconstructionofthispeptide,theproperlyorientedstructurecanbefoundhere. Executepdb2gmxbyissuingthefollowingcommand: pdb2gmx-fKALP-15_princ.pdb-oKALP-15_...
the preprocessor copies each molecule as needed. There is no limitation on the number of molecule types. Bonds and bond-angles can be converted into constraints, separately for hydrogens and heavy atoms. Then a coordinate file is read and velocities can be generated from a Maxwellian distribution...