Re: [AMBER] Tip3p water box size for two different systems.

From: Saman Yousuf ali <>
Date: Fri, 12 May 2017 05:30:43 +0000 (UTC)

Dear Martis,Thanks for response. I do not want to use same box size, I understand that as system size increase water box size should be bigger.  I am just asking about box size idea for my system. like if I generate 8 angstrom tip3p box around my monomeric system then what is the ideal box size for dimer? I hope you get my point.


    On Friday, May 12, 2017 10:19 AM, Elvis Martis <> wrote:

Since the proteins will be bigger, the box size will automatically be bigger if you use solvation shell method (using buffer).
However, I don't see a need why you must keep the box size same.

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Saman Yousuf ali []
Sent: Thursday, May 11, 2017 8:27 PM
Subject: [AMBER] Tip3p water box size for two different systems.

Dear All,
I am interested to simulate complex protein system in dimeric and monomeric form separately. Residues in case of monomeric system is 1-268 including one Ligand and cofactor. Dimeric system is double in size. My question is for solvation of each systems tip3p water size should be same for both? or dimeric system box size must be bigger in size as compared to monomer?



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Received on Thu May 11 2017 - 23:00:02 PDT
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