[AMBER] 1D-RISM in AmberTools: atom order in output, a bug?

From: Andrey Frolov <frolov.mis.mpg.de>
Date: Thu, 08 Jul 2010 17:04:06 +0200

Dear NAB and 3D-RISM Developers,

I have calculated the system of TIP3P water, Cs and Cl ions. So i have 4
atoms: O, H, Cs and Cl. They can be indexed by: S1A1, S1A2, S2A1, S3A1.
(where S stands for SPECIES and A for ATOMS).

It seems to me that the atom ordering in the potential output is
incorrect. When in the input to 1drism i put " OUTLST='xU' ", i get in
the output.uvv file the order of atom pairs potential:
 ivv iat1 iat2
  1 S1A1 S1A1
  2 S1A1 S1A2
  3 S1A1 S2A1
  4 S1A1 S3A1
  5 S1A2 S1A2
  6 S1A2 S2A1
  7 S1A2 S3A1
  8 S2A1 S2A1
  9 S2A1 S3A1
10 S3A1 S3A1

This order in output was generated with the following loops:
  do isp=1,nsp
     do iat=1,nat(isp)
        do isp2=isp,nsp
           do iat2=1,nat(isp2)

BUT!!! The true potential order is generated with these loops:
    ivv = 0
      do iv2=1,nv
         do iv1=1,iv2
            ivv = ivv + 1

Which gives the following TRUE ordering:
 ivv iat1 iat2
  1 S1A1 S1A1
  2 S1A2 S1A1
  3 S1A2 S1A2
  4 S2A1 S1A1
  5 S2A1 S1A2
  6 S2A1 S2A1
  7 S3A1 S1A1
  8 S3A1 S1A2
  9 S3A1 S2A1
10 S3A1 S3A1

I very hope that this is mixed up only in the potential output.

Is it really a bug or i misunderstood something?
Is this mistake present only in the potential output?
Could it affect the order of susceptibility functions in the input for

Thank you very much.
Andrey Frolov, PhD student at Max Planck Institute for Mathematics in
the Sciences, Germany

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Received on Thu Jul 08 2010 - 08:30:03 PDT
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