Solution LAB2 guanine - Revision history

Andrea Ferretti at 09:28, 26 March 2021

2021-03-26T09:28:22Z

← Older revision		Revision as of 09:28, 26 March 2021
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	* Back to the previous page: [[Electronic properties of isolated molecules#Exercise 1]]		* Back to the previous page: [[Electronic properties of isolated molecules#Exercise 1]]

	==Step 1==		==Step 1: geometry building==
	* Once you have Avogadro installed, open it and let's use the molecular builder to visualise a Guanine molecule:		* Once you have Avogadro installed, open it and let's use the molecular builder to visualise a Guanine molecule:

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	==Step 2==		==Step 2==
	Now we are ready to perform a ~~QM relaxation~~. As a first step, update your pseudo potentials directory by using git commands:		Now we are ready to perform a DFT simulations. As a first step, update your pseudo potentials directory by using git commands:

	git pull		git pull
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	new pseudo potentials (Nitrogen and Oxygen) will be downloaded in your pseudo potential directory.		new pseudo potentials (Nitrogen and Oxygen) will be downloaded in your pseudo potential directory.

	Create a ~~relax~~ input file (~~guanine_relax~~.in) paying attention to:		Create a scf input file (guanine_scf.in) paying attention to:
	~~forc_conv_thr = 1.0d-3 #we set a low threshold in order to not have a too long calculation~~
	ibrav=8 #orthorombic cell with vacuum		ibrav=8 #orthorombic cell with vacuum
	celldm(1) = 25.00		celldm(1) = 25.00
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	ATOMIC_POSITIONS (angstrom)		ATOMIC_POSITIONS (angstrom)

	'''Important''': How many '''k'''-points you need?		'''Important''':
			* How many '''k'''-points you need?
			* the amount of vacuum needs to be converged
			* same for the kinetic energy cutoff (note that here we can use the value of the total force as a convergence parameter)

			# ecutwfc Ry
			40 Total force = 0.316709 Total SCF correction = 0.000067
			50 Total force = 0.315474 Total SCF correction = 0.000089
			60 Total force = 0.319550 Total SCF correction = 0.000100
			80 Total force = 0.322261 Total SCF correction = 0.000098
			100 Total force = 0.323131 Total SCF correction = 0.000119
			120 Total force = 0.323153 Total SCF correction = 0.000140

			Despite 60-80 Ry seem to be appropriate, here we decide to use <code>ecutwfc=50</code> in order to keep the calculation time under control.


			==Step 3==
			We can now run a QM relaxation using DFT.
			Edit the input file according to:
			&CONTROL
			[...]
			calculation="relax"
			etot_conv_thr=1.0D-4
			forc_conv_thr=1.0D-3
			# we set a medium-tight threshold in order not to have a too long calculation
			/
			and add the <code>&IONS</code> namelist.

	Run the relaxation, it will take a while to rearrange the atoms in the relaxed positions according to the threshold parameter.		Run the relaxation, it will take a while to rearrange the atoms in the relaxed positions according to the threshold parameter.

Daniele Varsano at 20:26, 18 March 2021

2021-03-18T20:26:39Z

← Older revision		Revision as of 20:26, 18 March 2021
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	* Back to the previous page: [[Electronic properties of isolated molecules#~~Exercise1~~]]		* Back to the previous page: [[Electronic properties of isolated molecules#Exercise 1]]

	==Step 1==		==Step 1==

Andrea Ferretti: /* Step 1 */

2021-03-18T18:41:13Z

Step 1

← Older revision		Revision as of 18:41, 18 March 2021
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	The result of your FF optimisation should look like the following		The result of your FF optimisation should look like the following

	[[File:Snapshot avogadro.png\|none\|~~350px~~\|top\|]]		[[File:Snapshot avogadro.png\|none\|400px\|top\|]]

	==Step 2==		==Step 2==

Andrea Ferretti: /* Step 1 */

2021-03-18T18:38:34Z

Step 1

← Older revision		Revision as of 18:38, 18 March 2021
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	The result of your FF optimisation should look like the following		The result of your FF optimisation should look like the following

			[[File:Snapshot avogadro.png\|none\|350px\|top\|]]

	==Step 2==		==Step 2==

Andrea Ferretti: /* Step 2 */

2021-03-18T18:37:45Z

Step 2

← Older revision		Revision as of 18:37, 18 March 2021
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	ATOMIC_POSITIONS (angstrom)		ATOMIC_POSITIONS (angstrom)

	'''Important''': How many k points you need?		'''Important''': How many '''k'''-points you need?

	Run the relaxation, it will take a while to rearrange the atoms in the relaxed positions according to the threshold parameter.		Run the relaxation, it will take a while to rearrange the atoms in the relaxed positions according to the threshold parameter.

	>pw.x < guanine_relax.in > guanine_relax.out &		$> pw.x < guanine_relax.in > guanine_relax.out &

	One the job has converged you can compare the initial position (Force Field relaxed) with the final ones (QM relaxed). You can use xcrysden to visualise the optimisation steps.		One the job has converged you can compare the initial position (Force Field relaxed) with the final ones (QM relaxed). You can use xcrysden to visualise the optimisation steps.

Andrea Ferretti: /* Step 1 */

2021-03-18T18:36:29Z

Step 1

← Older revision		Revision as of 18:36, 18 March 2021
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	==Step 1==		==Step 1==
	*Once you have Avogadro installed, open it and let's use the molecular builder to visualise a Guanine molecule:		* Once you have Avogadro installed, open it and let's use the molecular builder to visualise a Guanine molecule:

	Build --> Insert-->Fragment-->nucleobases-->guanine		Build --> Insert-->Fragment-->nucleobases-->guanine

	Click on the selection settings "arrow" and right click to visualise the molecule.		Click on the selection settings "arrow" and right click to visualise the molecule.
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	Clicking on manipulate settings "hand" you can then rotate the molecule.		Clicking on manipulate settings "hand" you can then rotate the molecule.

	*Now we perform a classical relaxation using an Avogadro built-in Force Filed		* Now we perform a classical relaxation using an Avogadro built-in Force Filed

	Extension-->Molecular Mechanics and we choose a FF		Extension-->Molecular Mechanics and we choose a FF
			Extension-->Optimize geometry

	~~Extension-->Optimize~~ geometry		In few steps we have our relaxed geometry that we can save in .xyz format using:

	~~In few steps we have our relaxed geometry that we can~~ save in .xyz ~~format using:~~		File-->Save as-->select .xyz format and save in your disk as guanine_FF.xyz

	~~File-->Save as-->select .xyz format and save in~~ your ~~disk as guanine_FF.xyz~~		The result of your FF optimisation should look like the following

	==Step 2==		==Step 2==

Daniele Varsano: /* Step 2 */

2021-03-18T13:14:03Z

Step 2

← Older revision		Revision as of 13:14, 18 March 2021
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	new pseudo potentials (Nitrogen and Oxygen) will be downloaded in your pseudo potential directory.		new pseudo potentials (Nitrogen and Oxygen) will be downloaded in your pseudo potential directory.

	Create a relax input paying attention to:		Create a relax input file (guanine_relax.in) paying attention to:
	forc_conv_thr = 1.0d-3 #we set a low threshold in order to not have a too long calculation		forc_conv_thr = 1.0d-3 #we set a low threshold in order to not have a too long calculation
	ibrav=8 #orthorombic cell with vacuum		ibrav=8 #orthorombic cell with vacuum
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	Run the relaxation, it will take a while to rearrange the atoms in the relaxed positions according to the threshold parameter.		Run the relaxation, it will take a while to rearrange the atoms in the relaxed positions according to the threshold parameter.

			>pw.x < guanine_relax.in > guanine_relax.out &

	One the job has converged you can compare the initial position (Force Field relaxed) with the final ones (QM relaxed). You can use xcrysden to visualise the optimisation steps.		One the job has converged you can compare the initial position (Force Field relaxed) with the final ones (QM relaxed). You can use xcrysden to visualise the optimisation steps.

Daniele Varsano: /* Step 2 */

2021-03-18T13:13:04Z

Step 2

← Older revision		Revision as of 13:13, 18 March 2021
Line 47:		Line 47:

	'''Important''': How many k points you need?		'''Important''': How many k points you need?

			Run the relaxation, it will take a while to rearrange the atoms in the relaxed positions according to the threshold parameter.
			One the job has converged you can compare the initial position (Force Field relaxed) with the final ones (QM relaxed). You can use xcrysden to visualise the optimisation steps.

			xcrysden --pwo guanine_relax.out

			you can reduce the dimensionality to 0D and choose the option: Display All Coordinates as Animation
			In this way you will have a movie of the molecule relaxation

Daniele Varsano: /* Step 2 */

2021-03-18T12:04:59Z

Step 2

← Older revision		Revision as of 12:04, 18 March 2021
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	Create a relax input paying attention to:		Create a relax input paying attention to:
	forc_conv_thr = 1.0d-4 #we set a low threshold in order to not have a too long calculation		forc_conv_thr = 1.0d-3 #we set a low threshold in order to not have a too long calculation
	ibrav=8 #orthorombic cell with vacuum		ibrav=8 #orthorombic cell with vacuum
	celldm(1) = 25.00		celldm(1) = 25.00

Daniele Varsano: /* Step 2 */

2021-03-18T12:04:46Z

Step 2

← Older revision		Revision as of 12:04, 18 March 2021
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	new pseudo potentials (Nitrogen and Oxygen) will be downloaded in your pseudo potential directory.		new pseudo potentials (Nitrogen and Oxygen) will be downloaded in your pseudo potential directory.

	Create a relax input paying attention to:		Create a relax input paying attention to:
			forc_conv_thr = 1.0d-4 #we set a low threshold in order to not have a too long calculation
	ibrav=8 #orthorombic cell with vacuum		ibrav=8 #orthorombic cell with vacuum
	celldm(1) = 25.00		celldm(1) = 25.00