Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms?

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 6 Dec 2011 20:07:23 -0500

On Tue, Dec 6, 2011 at 3:35 PM, Marc van der Kamp
<marcvanderkamp.gmail.com>wrote:

> Hi Jason,
>
> Yes, I think the student originally put them in one command, but played
> around as it didn't seem to work.
> I get the same prmtop (only timestamp differs) when I do use the combined
> command, and the correct atoms (all 4 ions) are selected by the mask.
>

When I diffed the 2 topologies you gave me, I got this:

$ diff -w 4ions.prmtop exclusions2.prmtop
1c1
< %VERSION VERSION_STAMP = V0001.000 DATE = 12/06/11 15:38:03 

---
> %VERSION  VERSION_STAMP = V0001.000  DATE = 12/06/11  13:59:27
8c8
<        4       4       0       0       0       0       0       0       2
      0
---
>       13       4       0       0       0       0       0       0       2
      0
25c25
<        1       1       1       1
---
>        6       4       2       1
91c91,92
<        0       0       0       0
---
>        2       2       3       3       4       4       3       3       4
      4
>        4       4       0
Clearly the exclusion atom list is different here.  (I've fixed parmed so
it doesn't duplicate identical exclusions like above (2 2 3 3 4 4 3 3 4 4 4
4 0 should be 2 3 4 3 4 4 0) but the results from sander remain the same).
>From the original prmtop I get the following in my mdout file:
   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1       1.0587E+07     4.5553E+07     1.1102E+08     Cl-         2
 BOND    =        0.0000  ANGLE   =        0.0000  DIHED      =
 0.0000
 VDWAALS = 10587886.4492  EEL     =     -469.5927  EGB        =
 0.0000
 1-4 VDW =        0.0000  1-4 EEL =        0.0000  RESTRAINT  =
 0.0000
>From the exclusions2.prmtop I get:
   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1       0.0000E+00     0.0000E+00     0.0000E+00     Na+         1
 BOND    =        0.0000  ANGLE   =        0.0000  DIHED      =
 0.0000
 VDWAALS =        0.0000  EEL     =        0.0000  EGB        =
 0.0000
 1-4 VDW =        0.0000  1-4 EEL =        0.0000  RESTRAINT  =
 0.0000
So I'm not quite sure why you were getting what you were getting.  Here's
my mdin file:
input file
&cntrl
   imin=1, maxcyc=1, ntb=0, igb=6, cut=9999,
/
Thanks in advance for your help!
> Marc
> PS I note that exclusions2.prmtop is a lot smaller than the original
> 4ions.prmtop, but I don't think this is the problem
>
This is due to whitespace.  leap prints every line in the prmtop file with
80 characters (filling the empty ones with spaces).  parmed does not have
those spaces, which is why the file size is smaller.
All the best,
Jason
-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 06 2011 - 17:30:02 PST
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