AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: Abhishek Banerjee (a.banerjee_at_ymail.com)
Date: Thu Oct 08 2009 - 22:41:02 CDT

hi Francois
                     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. 
Thanks
abhishek 

--- 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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