From: Philip Peartree (P.Peartree_at_postgrad.manchester.ac.uk)
Date: Mon Sep 03 2007 - 16:18:22 CDT
Thanks Cesar, I have found that the box does shrink, I'm starting with a 12
angstrom boundary at all sides of the box, so hopefully that will be ok.
Quoting Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>:
> Sorry for the late response. I was out of town last week. I would
> like to add a little tip. If you are going to solvate your protein
> using vmd's solvate plugin, you should be aware that the box is going
> to shrink during equilibration.
> When building your system you might want to use a solvation box
> larger than the longest atom-atom distance plus the cutoff.
> Regards
> Cesar
>
> Vincent Kraeutler escribió:
>> this is only partially correct. if you use a nonbonded method like PME,
>> your molecule is in fact guaranteed to see (the electrostatic aspect of)
>> the nearest image of itself and in fact all periodic copies.
>>
>> your box size should therefore aim to satisfy the following properties:
>>
>> a) as guillaume mentioned, in many (but not all) cases, you want to
>> avoid LJ-interactions between the molecule and its nearest images. your
>> minimum box diameter should therefore be larger than the longest
>> atom-atom distance (at any time during the simulation) in your molecule
>> plus the cutoff. it's not always easy to predict how your molecule will
>> behave, so just make a good guess.
>>
>> b) regarding the electrostatics: the interactions between nearest images
>> should be small. if you employ criterion a), this is typically the case if:
>> -- your molecule has no net charge and the dipole moment of your
>> molecule is not huge.
>> -- your molecule has a net charge and you have a significant number of
>> ions, such that the overall charge of your system is zero.
>>
>> if you want to read up on this, i suggest:
>> http://www.igc.ethz.ch/phil/research/research.html
>>
>> cheers,
>> v.
>>
>> Guillaume LETELLIER wrote:
>>
>>> hi Philip
>>>
>>> The answer depends on your molecule flexibility and simulation
>>> parameters.
>>>
>>> You must prevent your moldecule from seeing images of itself generated
>>> by periodic conditions.
>>> Therefore, your molecule should never approach the box edge beyond a
>>> margin of half your cutoff distance.
>>>
>>>
>>> Philip Peartree a écrit :
>>>
>>>> Hi,
>>>>
>>>> I am running a simulation of a protein, and I wish to solvate in TIP3
>>>> waters.
>>>> What would be the recommended distance from the protein to the edge
>>>> of the
>>>> periodic box that I need to solvate? Is 12 angstroms enough or would you
>>>> recommend more?
>>>>
>>>> Philip Peartree
>>>>
>>>>
>>>
>>
>>
>>
>
>
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