AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Oct 08 2009 - 23:08:59 CDT

Abhishek,

>                      Thanks for you help.  Fast trick actually
> worked for me but still it is not very homogeneous. I am sending you
> the screenshot. How can I go for small box roughly for 216 dmf
> molecule. Because 30 A box contains ~900 molecule. 

"not very homogeneous" - after which step ?

You should minimize the box, and then run MD simulation using constant
volume and constant pressure conditions. You will finally have to
reimage your box using ptraj.

In our case, we equilibrated a 30 Ang. box. You could try using 15 or
20 Ang. & see how it goes... Then, once the box is built you can
obviously use a 10 Ang. buffer to solvate your molecule.

May be others in the list used different approaches...

regards, Francois

> --- On Wed, 7/10/09, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>
> From: FyD <fyd_at_q4md-forcefieldtools.org>
> Subject: Re: [AMBER] DMF solvent box
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Wednesday, 7 October, 2009, 8:34 PM
>
> Dear Abhishek,
>
>>                      DMF box again. I was trying to minimize the
>> box  but after minimization I saw there was a gap in the middle of
>> the  box. I am sending the script and screenshot of the box.
>> min.png  after minimization and ori.png I created with xleap.  Plz
>> help
>
> Sorry for the delay, but I had to look back in my notes because we
> encountered the same problem you have ;-) I even saved a picture
> (like you did) with this empty 'cross' in the middle of the box...
> This is not a big deal but you need to find the correct trick(s) to
> solve this.
>
> 1) what command did you use to solvate your DMF box ? could you try
> using a large buffer i.e. "30" (instead of the "10" value reported
> in the manual) - something like:
>
> SolvateBox DMF DMF 30
>
> 2) what command did you use for the setbox command ?
>
> Could you try to use "setBox DMF vdw" ?
> (to be done after the SolvateBox command)
>
> Does it solve your problem ?
>
> regards, Francois
>
>
>> --- On Sat, 19/9/09, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>>
>> From: FyD <fyd_at_q4md-forcefieldtools.org>
>> Subject: Re: [AMBER] DMF solvent box
>> To: "AMBER Mailing List" <amber_at_ambermd.org>
>> Date: Saturday, 19 September, 2009, 6:36 AM
>>
>> Hi Abhishek,
>>
>>> Now I want to equilibrate the box (at 298K and 1 atm pressure)
>>> to   get the correct density.  Then I will mix it with MEOH. How
>>> to do   it. Thanks for your great help.
>>
>> I would first minimize the box, then equilibrate at constant
>> volume  and then at constant pressure. regards, Francois

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