Difference between revisions of "Using GMIN to generate endpoints"
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import>Jmc49 (New page: We can use GMIN to explore the energy landscape of our peptide and find interesting structures (endpoints) to connect using OPTIM and PATHSAMPLE. Copy the '''coords.prmtop''' a...) |
import>Ss2029 |
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| − | We can use [[GMIN]] to explore the energy landscape of our peptide and find interesting structures (endpoints) to connect using [[OPTIM]] and [[PATHSAMPLE]]. Copy the '''coords.prmtop''' and '''coords.inpcrd''' |
+ | We can use [[GMIN]] to explore the energy landscape of our peptide and find interesting structures (endpoints) to connect using [[OPTIM]] and [[PATHSAMPLE]]. Copy the '''coords.prmtop''' and '''coords.inpcrd''' files you just made into a new directory, and add the following file: |
'''data''' - the GMIN input file |
'''data''' - the GMIN input file |
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| + | The line "igb .." species the Generalized Born implicit solvent model used. For vacuum, use igb=0 and delete "saltcon" keyword. |
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'''min_md.in''' - the [[AMBER]] (SANDER) settings for molecular dynamics (used to generate new conformations for basin-hopping) |
'''min_md.in''' - the [[AMBER]] (SANDER) settings for molecular dynamics (used to generate new conformations for basin-hopping) |
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Latest revision as of 15:19, 24 May 2011
We can use GMIN to explore the energy landscape of our peptide and find interesting structures (endpoints) to connect using OPTIM and PATHSAMPLE. Copy the coords.prmtop and coords.inpcrd files you just made into a new directory, and add the following file:
data - the GMIN input file
COMMENT DEBUG SLOPPYCONV 1.0D-5 TIGHTCONV 1.0D-6 MAXERISE 1.0D-4 DUMPINT 100 UPDATES 1000 MAXIT 20000 60000 MAXBFGS 1.0 TRACKDATA DUMPSTRUCTURES TEMPERATURE 1.0 SAVE 20 STEPS 100 1.0 STEP 0.0 RADIUS 300 AMBERMDSTEPS AMBER9 coords.inpcrd inpcrd
See the GMIN documentation for the explanation of these keywords!
min.in - the AMBER (SANDER) settings for minimisation
STOP &cntrl imin = 1, ncyc = 1, maxcyc = 1, igb = 2, saltcon=0.1, ntb = 0, cut = 999.99, rgbmax = 25.0, ifswitch = 1 /
The line "igb .." species the Generalized Born implicit solvent model used. For vacuum, use igb=0 and delete "saltcon" keyword.
min_md.in - the AMBER (SANDER) settings for molecular dynamics (used to generate new conformations for basin-hopping)
STOP &cntrl imin = 0, tempi = 600.0, temp0 = 800.0, ntt = 3, gamma_ln = 3.0, nstlim = 1000, dt = 0.001, igb = 2, saltcon = 0.1, ntb = 0, ntpr = 1000, ntwx = 0,nrespa=1, cut = 999.99, rgbmax = 25.0, ifswitch = 1, /
You can run GMIN now to generate some low energy structures:
AMBGMIN &