Date: Thu, 8 Oct 2009 20:41:02 -0700 (PDT)
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.q4md-forcefieldtools.org> wrote:
From: FyD <fyd.q4md-forcefieldtools.org>
Subject: Re: [AMBER] DMF solvent box
To: "AMBER Mailing List" <amber.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.q4md-forcefieldtools.org> wrote:
>
> From: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] DMF solvent box
> To: "AMBER Mailing List" <amber.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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