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size of solvation box
#32642 09/22/13 03:56 AM
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recently, I performed MD for alanine dipeptide in water box. The population of the backbone dihedral angles (phi/psi) were quite different in water boxes with different size. we can fine PPII, alpha-R, alpha-L in cubic water box with its sidelength of 28, but in the box with its sidelength of 42, there were no population for alpha-L.
the force field are the same, and the CMAP is considered.
my question is, how did the box size affect the population of the backbone dihedral angles, and how to decide the most probable size of the solvation box?
thank you so much for your time!

Re: size of solvation box
ckc1117 #32643 09/22/13 08:33 AM
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It is unlikely that 28A or 42A side length would make a drastic difference for the alanine dipeptide. Are your results converged? There are tons of literature using this model system, you can try to reproduce some of it.
A series of converged simulations with increasing side lengths will tell you what is needed in order not to have a size dependence.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: size of solvation box
ckc1117 #32664 09/24/13 09:17 AM
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Thank you so much for your time, I'll check the literature and try to reproduce some of it.
ps: I've try 30 A and 42 A side length for ALAD in CHCl3, the dihedral distribution shows no big difference, but the MD of ALAD in 34 and 42A DMSO boxes are quite different.

Re: size of solvation box
ckc1117 #32665 09/24/13 03:44 PM
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The fundamental question is whether your simulations are converged; this must be established before your start making comparisons.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: size of solvation box
ckc1117 #32666 09/24/13 04:10 PM
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rmv Online Content
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Running replicate simulations, esp. starting from different molecular configurations, is one way to try to answer this question.


Rick Venable
computational chemist

Re: size of solvation box
lennart #32668 09/25/13 01:44 AM
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ckc1117 Offline OP
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Dear Prof. Lennart, I am sure the energy, the temperature, the presure and etc. are convered.

Re: size of solvation box
rmv #32669 09/25/13 01:56 AM
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ckc1117 Offline OP
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Thank you for your advice, I'll try it with other initio structure (the origin ALAD is extended).

Re: size of solvation box
ckc1117 #32670 09/25/13 05:09 AM
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Yes, but is the conformational distribution converged?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: size of solvation box
lennart #32674 09/26/13 10:12 AM
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ckc1117 Offline OP
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Dear sir, I am sorry that I don't know how to make sure the conformational distribution was converged, does it have another criterion ?

Re: size of solvation box
ckc1117 #32675 09/26/13 10:39 AM
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AS Rick said, run several independent simulations and see if your distributions are the same; if you have a long simulation you can see if the distributions obtained using different parts of the trajectory are the same. Ideally you should have multiple transitions between the accessible conformations.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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