Re: [AMBER] not getting correct density for N,N-dimethylformamide

From: David A Case <>
Date: Mon, 9 Dec 2013 16:16:33 -0500

On Sat, Dec 07, 2013, Sohag Biswas wrote:

> Hi, I am Sohag Biswas, from Indian Institute of Technology Hyderabad,
> India. I am trying to simulate 1200 DMF molecules by using OPLS-AA
> parameters. After 5000 cycle minimization and 400 ps NVT running, I ran 3ns
> NPT simulation. But I am not getting the exact density. the density value
> is showing 0.7789 which is less than experimental value (0.93). Please
> somebody help me to solve this problem. Here I have given my frcmod and
> prepi input. Thank you. Yours sincerely.

How did you generate the frcmod file? I'm thinking that OPLS-AA may have
different mixing rules for Lennard-Jones terms than does Amber, so it might be
rather more complicated to create the appropriate Amber inputs.

Also, do you know that OPLS-AA gives a good density for DMF (compared to

I'm cc-ing this to Junmei Wang: the next version of GAFF will have much more
extensive calibration against organic liquid densities. I don't know if this
includes DMF or not.


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Received on Mon Dec 09 2013 - 13:30:02 PST
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