Re: [AMBER] problem with TI calculations

From: David A Case <>
Date: Wed, 21 Sep 2011 07:50:38 -0400

On Tue, Sep 20, 2011, Victor Ma wrote:
> I'm doing an one-step TI calculations for a single atom ligand mutation (H
> -> F). There are sort of two issues. The first one is as follows:
> ***** System must be very inhomogeneous.
> ***** Readjusting recip sizes.
> In this slab, Atoms found: 1861 Allocated: 1781
> This seems like a warning message and does not really stop the simulation.
> And I see this from the first step of minimization to the final production
> run. I did some research online. It could be a strange starting structure or
> density problem. I checked the energy of the first step minimization, it
> looks ok. There are no "******" values. One possibility is that I'm using
> ntc = 1 with TIP3P water. So I switched to ntf=2, ntc=2. It didn't help.
> The other problem is this:
> * NB pairs 231 1594826 exceeds capacity ( 1594870) 7
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f

These are probably related. I'd suggest fully equilibrating (including the
NTP part) one of the systems (i.e. with icfe=0), then using that structure to
start the TI simulation. Of course, at each lambda value, you will need an
addtional (short) equilibration phase, but by that time you should have
resolved any problems with inhomogeneity, etc.

(Also, be very careful in combining ntp=1 and ntr=1; adding icfe=1 to the
mix just makes the whole thing more complex. Be sure you really need
restraints on your system.)

...good luck...dac

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Received on Wed Sep 21 2011 - 05:00:03 PDT
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