From: Madhulika Gupta (gmadhulika1909_at_gmail.com)
Date: Sat May 21 2016 - 10:20:34 CDT
Dear Mam,
Thank you so much for your kind reply. You are always a great help!
Thanks again
Regards
On Sat, May 21, 2016 at 2:47 PM, Ana Celia Vila Verde <
acavilaverde_at_gmail.com> wrote:
> Dear Madhulika,
>
> I don't think there's anything in principle wrong with your NAMD
> simulations in vaccuum. It is to be expected that the adsorption energy of
> a protein onto a surface in the absence of solvent should be very different
> from that calculated in the presence of solvent (even when using the same
> force field).
>
> I hope this helps,
>
> Ana
>
> On 20/05/16 13:01, Madhulika Gupta wrote:
>
> Dear All,
> I am trying to study protein adsorption on metal surface in vacuum in
> NAMD. I am getting almost double the adsorption energies values as that in
> explicit water and DFT studies.
> I am not sure if there is a different method to treat electrostatics and
> van der Waal forces in vacuum. I am using PME off and a cutoff of 12 A for
> 45X45X45 A box.
> Please advise as to how should I modify the vacuum simulations to get
> better results in namd?
>
>
> Thanks and Regards
> Madhulika
>
> --
> Madhulika Gupta
> Research Scholar
> Department of Chemistry
> Indian Institute of Technology, Delhi
> New Delhi-110016
>
>
>
-- Madhulika Gupta Research Scholar Department of Chemistry Indian Institute of Technology, Delhi New Delhi-110016
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