8 Angstroms seems small in both cases. I would consider 10, since the
system will shrink on equilibration, as inititial vdw voids go away.
Bil;
On 5/11/17 10:42 PM, Elvis Martis wrote:
> Hi,
> There is nothing idea here.
> You can use 8 angstrom buffer for both your dimer and your monomer and there should be no problem.
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/>
>
>
>
>
>
> From: Saman Yousuf ali [mailto:saman.yousufali64.yahoo.com]
> Sent: Friday, May 12, 2017 11:01 AM
> To: Elvis Martis <elvis.martis.bcp.edu.in>; AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Tip3p water box size for two different systems.
>
> 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.
>
> Thanks
>
>
>
> On Friday, May 12, 2017 10:19 AM, Elvis Martis <elvis.martis.bcp.edu.in<mailto:elvis.martis.bcp.edu.in>> wrote:
>
> Hi,
> 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
> W www.elvismartis.in<http://www.elvismartis.in>
> Skype. adrian_elvis12
>
>
>
> -----Original Message-----
> From: Saman Yousuf ali [mailto:saman.yousufali64.yahoo.com<mailto:saman.yousufali64.yahoo.com>]
> Sent: Thursday, May 11, 2017 8:27 PM
> To: amber.ambermd.org<mailto:amber.ambermd.org>
> 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?
>
> Thanks
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 11 2017 - 23:00:03 PDT
