Re: [AMBER] enquiry regarding latest Amber

From: Divi/GMAIL <>
Date: Sat, 25 Jan 2014 13:14:55 -0500

  Hi Ved:
  I am not sure you can get a high end system for 3K. but you can get a
decent GPU workstation.
  My suggestion is to get a workstation that is dual processor (hexacore or
quad-core, depending on prices in India) system with motherboard that
supports dual PCIE-3 lanes (X16/X16).
  You can get two GTX-780 cards to go with the system and 16 or 32GB memory.
These cards are about Rs. 50,000 in India. Make sure you get 1200 Watts
Gold certified Power supply from the Vendor (if you are not building

   My personal choice is not to buy Gaussian that in my opinion is waste of
money given your budget limit. Rather, you can get NWCHEM or GAMESS free.
Both codes would do almost everything that GAUSSIAN does. I have NWCHEM and
GAUSSIAN in my lab. Unix friendly students use NWCHEM and GUI driven
click-and-submit students like GAUSSIAN (on Windows). Both programs get the
job done.

   I built myself several GPU workstations in my lab including GTX780 and
TITAN's for anywhere from USD2500 to 3200. They are running perfect 24/7
for the past one year.

  Hope it helps, Feel free to shoot an email if you have more questions.


-----Original Message-----
From: Ved Prakash
Sent: Saturday, January 25, 2014 11:14 AM
Subject: [AMBER] enquiry regarding latest Amber


We are planning to buy a high end computing system for carrying out MD
simulations on molecular systems as large as a few hundred atoms (mostly
nucleic acids with small organic fluorophores covalently attached to them).
Apart from this, we also plan to carry out DFT level calculations on
similar molecular systems (mostly biological molecules) using "Gaussian".

It would be great if you can help us out with the best version of Amber and
the optimized system configuration (for example processor, RAM, etc.) for
carrying out such calculations. Our budget for the computing system
(excluding software) is around USD 3,000.
Best wishes
Ved Prakash
Research Scholar
Dr. Yamuna Krishnan's Lab
National Centre for Biological Sciences
Tata Institute of Fundamental Research
GKVK, Bellary Road,
Bangalore 560065, India
Phone: 09632160081
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Received on Sat Jan 25 2014 - 10:30:02 PST
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