Re: [AMBER] Enquiry regarding MD run

From: Jason Swails <>
Date: Wed, 3 Mar 2010 01:04:23 -0500

On Wed, Mar 3, 2010 at 12:42 AM, bharat lakhani <> wrote:
> running minimisation prior to simulation,previous charge for the system was
> 13.37,added Cl- 0 ions, present charge is  0.378,its not getting zero and

I'm not sure how you're getting a non-integral charge. But right here
it says your system charge is 13.37 prior to adding 13 Cl- ions (which
will bring the charge down to 0.37). I'm guessing that you derived
charges using antechamber (?) or something else for some type of
capped residue? Then just removed the caps? That's certainly one way
of messing up your charge, if the charge of your *neutral* caps is
non-zero, then you're effectively subtracting or adding fractions of
electrons to the fragment you're actually using.

Of course this is all speculative, since there are an infinite number
of ways of getting whatever charge for whatever system you want. If
this was your problem, then re-derive your charges by constraining the
charges given to your caps appropriately (I believe R.E.D. can do
this, and I'm sure Francois can point you to a couple tutorials to
help get you started).

If this is not your problem, then you'll need to reply with more
details about your system and the steps you took to set it up.

Good luck!
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Tue Mar 02 2010 - 22:30:03 PST
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