Using GMIN to generate endpoints - Revision history

import>Ss2029 at 15:19, 24 May 2011

2011-05-24T15:19:30Z

← Older revision		Revision as of 15:19, 24 May 2011
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	</pre>		</pre>

	The line "igb .." species the Generalized Born implicit solvent model used. For vacuum, use igb=0 and delete 'saltcon'.		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)		'''min_md.in''' - the [[AMBER]] (SANDER) settings for molecular dynamics (used to generate new conformations for basin-hopping)

import>Ss2029 at 15:18, 24 May 2011

2011-05-24T15:18:57Z

← Older revision		Revision as of 15:18, 24 May 2011
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	/		/
	</pre>		</pre>

			The line "igb .." species the Generalized Born implicit solvent model used. For vacuum, use igb=0 and delete 'saltcon'.

	'''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)

import>Ss2029 at 17:07, 20 April 2011

2011-04-20T17:07:15Z

← Older revision		Revision as of 17:07, 20 April 2011
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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''' ~~giles~~ you just made into a new directory, and add the following file:		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

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...

2011-03-14T14:49:37Z

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...

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''' and '''coords.inpcrd''' giles you just made into a new directory, and add the following file:

'''data''' - the GMIN input file
<pre>
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
</pre>
See the [[GMIN]] documentation for the explanation of these keywords!

'''min.in''' - the [[AMBER]] (SANDER) settings for minimisation
<pre>
STOP
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 2, saltcon=0.1,
ntb = 0,
cut = 999.99,
rgbmax = 25.0,
ifswitch = 1
/
</pre>

'''min_md.in''' - the [[AMBER]] (SANDER) settings for molecular dynamics (used to generate new conformations for basin-hopping)
<pre>
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,
/
</pre>
You can run [[GMIN]] now to generate some low energy structures:
<pre>
AMBGMIN &
</pre>