Re: [AMBER] TIP3p lennard jones parameters

From: David A Case <>
Date: Fri, 25 Aug 2017 16:17:08 -0400

On Fri, Aug 25, 2017, Lizelle Lubbe wrote:

> I noticed that the TIP3P parameters in this file do not correspond to
> the literature (radius 3.15061; well depth 0.6364)
> My values are 1.7683 and 0.1520 respectively.

Your "literature" values are sigma (in ) and epsilon (in kJ/mol). Amber
uses Rmin/2 (in ) and epsilon in kcal/mol. If you convert to what
Amber uses, you will find that they match.

> If not, how can I increase the verbosity in to come to the
> bottom of this?

I agree that there are situations where it would be quite helpful if
parmed could print more information when it finds problems. Volunteers
are hereby solicited.

> source leaprc.ff14SB

General advice: upgrade to AmberTools17. Second, if you think that your
water model might be leading to off-diagonal LJ parms, do some exploring:
make a prmtop with just water (for example), and see what parmed says. Keep
adding in components one by one to see if you can isolate the problem.

...good luck....dac

AMBER mailing list
Received on Fri Aug 25 2017 - 13:30:06 PDT
Custom Search